Index (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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B

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G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
GaussianBlur2D() - Constructor for class GaussianBlur2D
GaussianCumulative<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
GaussianCumulative() - Constructor for class GaussianCumulative
GaussianSampler - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar: Samples from a Gaussian distribution whose parameters are determined by a Dictionary.
GaussianSampler() - Constructor for class GaussianSampler
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawCroppedObjectsGenerator
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawObjectsGenerator
generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface AddCriteria
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaEnergyPair
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaNever
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
generateIntersectingObjects(int, int, boolean) - Static method in class IntersectingCircleObjectsFixture: Generates a number of circles that intersect and don't intersect
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
GenerateLabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature: Generates a list of header-names for columns unrelated to features (identifiers and groups)
GenerateLabelHeadersForCSV(String[], Optional<String>) - Constructor for class GenerateLabelHeadersForCSV
generateMasks(ObjectCollectionWithProperties) - Method in class DrawCroppedObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class DrawObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator
generateNormal(double, double) - Method in interface RandomNumberGenerator: Generates a Gaussian (Normal) random variable with particular parameterization.
generateNormal(double, double) - Method in class RandomNumberGeneratorMersenne
generatePoisson(double) - Method in interface RandomNumberGenerator: Generates a Poisson random variable with particular parameterization.
generatePoisson(double) - Method in class RandomNumberGeneratorMersenne
generateProperties(Optional<Resolution>) - Method in class Ellipse
generateProperties(Optional<Resolution>) - Method in class Ellipsoid
generateProperties(Optional<Resolution>) - Method in class Mark
generateProperties(Optional<Resolution>) - Method in class MarkWithPosition
generateProperties(Optional<Resolution>) - Method in class OverlayMark
generateProperties(Optional<Resolution>) - Method in class OverlayObjectMask
generateProperties(Optional<Resolution>) - Method in class Overlay
GenerateString - Class in org.anchoranalysis.image.io.bean.stack.combine
GenerateString(String) - Constructor for class GenerateString
GenerateString() - Constructor for class GenerateString
GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider: Generates colors to match the size of an object-collection
GenerateToMatchObjects() - Constructor for class GenerateToMatchObjects
GenerateUniqueParameterization - Interface in org.anchoranalysis.bean: Objects that must implement well-defined equals() and hashCode() methods and also generate a name uniquely identifying the class and all parameterization
generator() - Static method in class ObjectCollectionWriter
Generator<T> - Interface in org.anchoranalysis.io.generator: A class that writes a particular type of object(s) to the filesystem.
GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator: Exposes a Generator<T> as if it was an Generator<S>.
GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator: Settings and methods for writing to the filesystem from a generator.
Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
Geometry() - Constructor for class Geometry
Geometry(double, double) - Constructor for class Geometry
get(Class<? extends T>) - Method in class BeanInstanceMap
get() - Method in class CachedSupplier
get(K) - Method in class LRUCache
get(int) - Method in interface ColorIndex
get(int) - Method in class ColorIndexModulo
get(int) - Method in class ColorList
get(int) - Method in class SingleColor
get() - Method in class WithPriority
get() - Method in interface CheckedSupplier: Applies a supplier like with Supplier.get().
get() - Method in interface StoreSupplier: Gets the object being supplied to the store
get(int) - Method in class BoundedIndexContainerFromList
get(int) - Method in class BoundsFromRange
get(int) - Method in class BoundedIndexContainerBridge
get(int) - Method in class IntegerSequenceContaner
get(int) - Method in class SingleContainer
get(int) - Method in interface GetterFromIndex
get(Progress) - Method in class CachedProgressingSupplier
get(Progress) - Method in interface CheckedProgressingSupplier
get() - Static method in class ProgressIgnore
get(int) - Method in class FeatureList
get() - Method in interface SessionInput: Returns the underlying feature-input (independent of the session)
get(int) - Method in class FeatureNameList
get(int) - Method in class ResultsVector
get(int) - Method in class ResultsVectorList
get() - Method in interface CacheSupplier
get() - Method in class SessionInputSequential
get(int) - Method in class NamedFeatureStore
get(String) - Method in class NamedFeatureStore
get(int) - Method in class BoundingBoxesOnPlane
get(int, int) - Method in class TableItemArrangement
get(int) - Method in class ObjectCollectionWithProperties
get(int) - Method in class SeedCollection
get(int) - Method in class ContiguousVoxelPath
get(Progress) - Method in interface NamedStacksSupplier
get(int) - Method in class TimeSequence
get(String) - Method in class NamedEntries
get(Progress) - Method in interface TimeSequenceSupplier
get(int) - Method in class StackSeries
get(VoxelDataType) - Method in class VoxelDataTypeFactoryMultiplexer: Multiplexes one of the factories according to data-type
get(int) - Method in class ObjectCollection
get(int) - Method in class VoxelsWrapperList
get(int) - Method in interface DestinationChannelForIndex
get() - Method in interface PathSupplier
get(int) - Method in class DeriveElementsFromSequencedDirectory
get() - Method in class FinderDictionary
get() - Method in class FinderFileAsText
get() - Method in class FinderSerializedObject
get() - Method in interface SerializedObjectSupplier
get(Optional<String>) - Method in class InputOutputContextSubdirectoryCache: Gets (from the cache if it's already there) a context for a subdirectory of given-name
get() - Method in interface ElementSupplier: Gets/creates the element to be written.
get() - Method in interface ElementWriterSupplier: Gets/creates the ElementWriter to be used for an output.
get(int) - Method in class RunningSumCollection: An individual item in the collection.
get(int) - Method in class ImageMoments
get(int) - Method in class MarksWithTotalEnergy
get(int) - Method in class EnergySavedInd
get(String) - Method in class EnergySchemeSet
get(int) - Method in class MemoList
get(int) - Method in class UpdatableMarksList
get(int) - Method in class IndexByChannel
get(String) - Method in interface MultiInputSubMap: Returns null if non-existent
get(String) - Method in class OperationMap
get(String) - Method in class StackWithMap
get(int) - Method in class MarkCollection
get(int) - Method in class WeightedKernelList
get(int) - Method in class AggIDCounter
get(int) - Method in class ColoredOverlayCollection
get(int) - Method in class OverlayCollection
get(T, int) - Method in interface GetForSeries
get(String) - Method in class GroupedAnnotationLabels
get(int) - Method in class ListWithThumbnails
get() - Method in class PriorityQueueIndexRangeDownhill
get(T) - Method in class FileLabelMap
get() - Method in class DeserializedManifest
get(String) - Method in class IndexedCSVRows
get(String) - Method in class MapGroupToRow
get() - Method in interface FeatureResultSupplier
get(int) - Method in class BoundedList: Gets a particular element
getAboveMaxValue() - Method in class RangeCompareBase: Constant to return if outside the range (above the maximum allowed)
getAcceptAll() - Method in class Aggregator
getAdd() - Method in class VisualizeOnBackground
getAddCriteria() - Method in class RandomCollectionWithAddCriteria
getAdditionalBackgrounds() - Method in class MarkProposerStrategy: Additional background-stacks that are possible to use while annotating.
getAdditionalChannels() - Method in class MultiInputManagerQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalChannels() - Method in class NamedChannelsQuick: Additional channels other than the main one, which are located in the main raster file
getAdditionalPropertyPaths() - Method in class PermutePropertyWithPath: Additional property paths that are also changed, along with the main propertyPath *
getAddSum() - Method in class GradientBaseAddSum: Added to all gradients (so we can store negative gradients)
getAdjacentChannels() - Method in class NamedChannelsQuick: Channels that are located in a separate raster file adjacent to the main raster file
getAfterPreoperation() - Method in class OverlappingObject: After pre-operation but before scaling
getAggInterval() - Method in class ReporterInterval
getAggIntervalLog10() - Method in class ReporterInterval: How many iterations before printing a new report? Encoded in log10.
getAggregateReceiver() - Method in class ReporterAggregate
getAggregateReceiver() - Method in class ConsoleAggregatedReporter
getAggregateReceiver() - Method in class CSVReporterAggregated
getAggregateReceiver() - Method in class Log4JReporter
getAggregateReceiver() - Method in class MemoryUsageReporter
getAggregateReceiver() - Method in class OptimizationStepLogReporter
getAggregateReceiver() - Method in class TextFile
getAggregateTriggerBank() - Method in class FeedbackBeginParameters
getAll() - Method in class MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
getAllCacheNames() - Method in class CacheTransferSourceCollection
getAllKernelFactories() - Method in class KernelProposer
getAllowsChildren() - Method in class ErrorNodeImpl
getAngle() - Method in class OrientationAxisAngle: Angle part of axis-angle orientation (in radians)
getAngleDegrees() - Method in class Orientation2D
getAngleDegrees() - Method in class AngleRotation
getAngleRadians() - Method in class Orientation2D
getAnnealScheme() - Method in class SimulatedAnnealing
getAnnotations() - Method in class FromAnnotations
getAnnotatorStrategy() - Method in class AnnotationInputManager
getAppendChannels() - Method in class NamedChannelsQuick: Channels that are located in a separate raster file somewhere else in the project's structure
getAppendCSV() - Method in class FromCSVInputManager
getAppendCsv() - Method in class MatchedAppendCsv
getAppendDictionary() - Method in class MultiInputManager
getAppendFilePath() - Method in class MultiInputManager
getAppendHistogram() - Method in class MultiInputManager
getAppendMarks() - Method in class MultiInputManager
getAppendMarksFromAnnotation() - Method in class MultiInputManager
getAppendMarksFromAnnotationAcceptedOnly() - Method in class MultiInputManager
getAppendMarksFromAnnotationRejectedOnly() - Method in class MultiInputManager
getAppendObjects() - Method in class MultiInputManager: Appends object-collections to the MultiInput.
getAppendStack() - Method in class MultiInputManager
getArbitraryElement() - Method in interface NamedProvider: Gets one element of the provider (arbitrarily)
getArrange() - Method in class ArrangeRaster
getArrange() - Method in class Cell
getArrange() - Method in class CombineRasterGenerator
getAsBoolean() - Method in interface CheckedBooleanSupplier: Applies a supplier like with BooleanSupplier.getAsBoolean().
getAsDouble(String) - Method in class Dictionary: Retrieves a value from the dictionary, and converts to a double.
getAssigner() - Method in class CompareAnnotations
getAssignMode() - Method in class SimulatedAnnealing
getAssociatedElementRange() - Method in class MutableDirectory
getAssociatedElementRange() - Method in interface SequencedDirectory: The associated element-range with ths folder.
getAssociatedMark() - Method in class ErrorNodeImpl
getAsString(String) - Method in class Dictionary: Retrieves a value from the dictionary as a String.
getAsSupplier(String) - Method in class NamedStacks
getAttributes() - Method in class StackWriteOptions: The attributes of the particular stack to write.
getAxis() - Method in class AxisAlignedUnitVector: Which axis the unit-vector will align with.
getAxis() - Method in class OrientationAxisAngle: Axis part of axis-angle orientation (should be normalized)
getAxis() - Method in class CenterOfGravity
getAxis() - Method in class GradientForAxis: Which axis? X=0, Y=1, Z=2
getAxis() - Method in class ForSpecificAxis
getAxis() - Method in class ArbitraryInsidePoint
getAxis() - Method in class BoundingBoxAlongAxisBase
getAxis() - Method in class GradientMeanForAxis
getAxis() - Method in class PrincipalAxisOrientation: Which axis to read from (x,y,z)
getAxis() - Method in class BoundingBoxExtent
getAxisColor() - Method in class PlotColorScheme
getAxisMax() - Method in class AxisLimits
getAxisMin() - Method in class AxisLimits
getBackground() - Method in class AnnotatorStrategy
getBackground() - Method in class ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
getBackground() - Method in class DualStack: The background
getBackground() - Method in class ColoredBase: The background.
getBackgroundChannelIndex() - Method in class OutlinePreserveRelativeSize: Uses only this channel (identified by an index in the stack) as the background, -1 disables.
getBackgroundChannelName() - Method in class CompareAnnotations
getBackgroundChannelProvider() - Method in class MorphologicalOperatorBase
getBackgroundColor() - Method in class PlotColorScheme
getBackgroundID() - Method in class VisualizeOnBackground
getBackgroundStackMap() - Method in class AnnotationBackground: If non-null, maps underlying stack-name to a background
getBackgroundStackName() - Method in class SegmentIntoMarks
getBaseName() - Method in class FilenameSplitExtension: The part of the filename without an extension.
getBeanExtension() - Method in class QuickMultiDatasetExperiment
getBeanExtension() - Method in class QuickMultiDatasetStructuredExperiment
getBeanName() - Method in class AnchorBean: A short-name identifying a bean (by default the name of the class associated with the bean).
getBelowMinValue() - Method in class RangeCompareBase: Constant to return if outside the range (below the minimum allowed)
getBest() - Method in class DualState
getBest() - Method in class OptimizationStep
getBestState() - Method in class Reporting
getBinaryInputChannelID() - Method in class AddDistanceTransform: The ID of the binary input mask that determines the region of the watershed
getBinarySgmn() - Method in class BinarySegmentByObject
getBirthRepeats() - Method in class KernelReplace
getBitsPerPixel() - Method in class ForceBitsPerPixel
getBlockSize() - Method in class HOGParameters: The block-size as per OpenCV implementation (identical default-size)
getBlockStride() - Method in class HOGParameters: The block-stride as per OpenCV implementation (identical default-size)
getBlue() - Method in class RGBColorBean
getBlue() - Method in class RGBColor
getBlue() - Method in class ThreeChannels
getBorderWidth() - Method in class MontageSlices: Adds a border around each part of the montage
getBoundRadius() - Method in class MarkWithPositionAndSingleRadius
getBounds() - Method in class RandomOrientation
getBoundType() - Method in class BoundChangeEvent
getBridgeMatcher() - Method in class Bridge: Used to match each input-object to an intermediary-object
getBundleSize() - Method in class ObjectSerializerPeriodicReporter
getBundleSize() - Method in class VoxelizedMarksChangeReporter
getCache() - Method in interface SessionInput
getCache() - Method in class CacheAndReuseStrategy
getCache() - Method in class SessionInputSequential
getCacheNames() - Method in class CacheTransferSource
getCacheSize() - Method in class RelationWithMatches: Size of feature evaluation cache for featureEvaluatorMatch
getCalculateLevel() - Method in class CalculateLevelOne
getCalculateLevel() - Method in class ThresholderGlobal
getCalculateLevel() - Method in class LevelPerObjectBase: Method to calculate the level for a particular object.
getCalculateLevel() - Method in class GreaterThanThreshold: Calculates the level for the threshold
getCalculateLevel() - Method in class LevelFromHistogram
getCalculateLevel() - Method in class ThresholdHistogram
getCalculateLevel() - Method in class CalculateLevelBase
getCalculateLevelElse() - Method in class CalculateLevelRelativeToThreshold
getCalculator() - Method in class NamedFeatureCalculatorMulti
getCellDefault() - Method in class Tile
getCells() - Method in class Tile
getCellSize() - Method in class HOGParameters: The cell-size as per OpenCV implementation (identical default-size)
getCenter() - Method in class SlidingBuffer: The buffer for the currently selected slice.
getCenterPoint() - Method in class FitResult
getCenterPointX() - Method in class EllipseStandardFormConverter
getCenterPointY() - Method in class EllipseStandardFormConverter
getChangedMarkIDArr() - Method in class KernelDescision
getChangedMarkIDs() - Method in class Reporting
getChannel(int) - Method in class EnergyStack
getChannel(int) - Method in class EnergyStackWithoutParams
getChannel() - Method in class ChannelProviderUnary
getChannel(int) - Method in class Stack
getChannel(int) - Method in class StackNotUniformSized
getChannel(String, int, Progress) - Method in class ChannelFilter
getChannel() - Method in class ChannelFilter
getChannel(String, int, Progress) - Method in interface ChannelGetter
getChannel(String, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
getChannel(String, int, Progress) - Method in class NamedChannelsForSeriesMap
getChannel() - Method in class FromChannel
getChannel() - Method in class FromChannel
getChannel() - Method in class FromChannelBase
getChannel() - Method in class IntensityGreaterEqualThan
getChannel() - Method in class UnaryWithChannelBase
getChannel() - Method in class WithChannelBase
getChannel() - Method in class FromChannelOrMask: A channel that is provided to the stack.
getChannel() - Method in class NamedChannel
getChannel(String) - Method in class ChannelGetterForTimepoint
getChannel1() - Method in class ChannelProviderBinary
getChannel1() - Method in class ChannelProviderTernary
getChannel2() - Method in class ChannelProviderBinary
getChannel2() - Method in class ChannelProviderTernary
getChannel3() - Method in class ChannelProviderTernary
getChannelAssignFrom() - Method in class AssignFromChannel
getChannelChecker() - Method in class GroupedSharedState
getChannelConversionStyle() - Method in class ConvertImageFormat: To convert as RGB or independently or in another way
getChannelConverter() - Method in class Convert
getChannelConverter() - Method in class ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
getChannelElse() - Method in class IfParamEquals
getChannelFilter() - Method in class ConvertImageFormat: Optionally, includes only certain channels when converting.
getChannelFirst() - Method in class Difference: Index of first channel
getChannelGroupID() - Method in class RegularExpression
getChannelID() - Method in class AddEdgeFilters: The ID of the channel that provides the input to the filter
getChannelIfVoxelZero() - Method in class IfVoxelZero: If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
getChannelIndex() - Method in class FromStack
getChannelIndex() - Method in class FromStackChannel
getChannelIndex() - Method in class One
getChannelIndex() - Method in class FileDetails
getChannelIndex() - Method in class MultiInputManagerQuick: If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
getChannelLookup() - Method in class NormalizeDifferenceToMedian
getChannelMap() - Method in class NamedChannels
getChannelMask() - Method in class ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelName() - Method in class ChannelFilter
getChannelName() - Method in class SingleChannel
getChannelName() - Method in class ConvertNamedChannelsToStack: By default all channels are converted into a stack.
getChannelNum() - Method in class SortedSetChannel
getChannelOptional(String, int, Progress) - Method in interface NamedChannelsForSeries: Gets a channel if it exists, returning empty if it doesn't
getChannelOptional(String, int, Progress) - Method in class NamedChannelsForSeriesConcatenate
getChannelOptional(String, int, Progress) - Method in class NamedChannelsForSeriesMap
getChannelSecond() - Method in class Difference: Index of second channel
getChannelsExtra() - Method in class ScoreVoxels
getChannelsPerByteArray() - Method in class ForceChannelsPerByteArray
getChannelThreshold() - Method in class ThresholdAgainstChannel
getChannelType() - Method in class ConsistentChannelChecker
getChart() - Method in class PlotInstance
getCheck() - Method in class Not
getChecked() - Method in class Outputter: Gets the underlying delegate of Outputter that throws checked-exceptions instead of using a ErrorReporter.
getCheckMark() - Method in class FromObjects
getCheckMark() - Method in class Check
getCheckMark() - Method in class Check
getCheckParsedFilePathBag() - Method in class GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
getChildAt(int) - Method in class ErrorNodeImpl
getChildCount() - Method in class ErrorNodeImpl
getClassifierProvider() - Method in class BinaryClassifierImageLabeller
getClassLabelsPath() - Method in class SegmentObjectsFromTensorFlowModel: Relative-path to the class-labels file, a text file where each line specifies a class label in order, relative to the models/ directory in the Anchor distribution.
getClassOfTarget() - Method in class ExtractFromParam
getCode(int) - Method in class EncodedIntBuffer
getCol(int) - Method in class TableItemArrangement
getCol() - Method in class Cell
getColForListIndex(int) - Method in class TableItemArrangement
getCollection() - Method in class KernelDeath.MarkAnd
getCollectionID() - Method in class ParamFromCollection
getColor() - Method in class FromSingle: The single color to repeat.
getColor(int) - Method in class ColoredOverlayCollection
getColor() - Method in class AnnotationLabel: An optional color associated with the label when displayed via GUI
getColor() - Method in class ColoredMask
getColorIDGetter() - Method in class ObjectDrawAttributes: Gets a color ID associated with the object
getColorIndex() - Method in class ObjectDrawAttributes: Colors for a given index
getColorList() - Method in class ColoredMarks
getColors() - Method in class ColorSchemeUnary: The delegate that creates the (unshuffled) list.
getColors() - Method in class FromList: The list of colors to specify
getColors() - Method in class ColoredOverlayCollection
getColors() - Method in class ColoredBaseWithGenerator: Colors to use for drawing objects
getColors() - Method in class ColoredObjectCollection: The colors in the collection.
getColorScheme() - Method in class GenerateToMatchObjects
getColorsUnpaired() - Method in class CompareAnnotations
getColorUnselectedObjects() - Method in class OutlinePreserveRelativeSize: Optionally outline the other (unselected for the thumbnail) objects in this particular color.
getColumnDefinition() - Method in class ExportObjectsFromCSV: Column definition for the CSV files
getColumnGroup() - Method in class ColumnDefinition: Name of CSV column used to group results (the same values, are outputted together)
getColumnID() - Method in class ColumnDefinition: Name of CSV column with the file identifier
getColumns() - Method in class MontageSlices: How many columns to use in the montage, or 0 to guess an approximately square output
getColumnUniquePixel() - Method in class ColumnDefinition: Name of CSV column with X coordinate of point for the first Object
getCombine() - Method in class FromObjects
getCombined() - Method in interface VoxelPartition
getCombined() - Method in class VoxelPartitionHistogram
getCommand() - Method in class MorphologicalOperation: One of: open, close, fill, erode, dilate, skel, outline
getCommandName() - Method in class HelpConfig: What the application command is described as in the help message e.g. anchor or anchorGUI
getComparerLeft() - Method in class AnnotationComparisonInputManager
getComparerMultiplex(boolean) - Method in class AnnotationComparisonInput
getComparerRight() - Method in class AnnotationComparisonInputManager
getComparers() - Method in class AnnotationComparisonInput
getCondition() - Method in class IfParamEquals
getCondition() - Method in class IfKeyValueCondition
getConfidence() - Method in class LabelledWithConfidence
getConfidence() - Method in class WithConfidence
getConfidenceThreshold() - Method in class ConditionallyMergeOverlappingObjects: The maximum difference in confidence for merging.
getConnPoint() - Method in class ContiguousVoxelPath
getConstant() - Method in class MaxWithConstant
getContains() - Method in class DescriptiveNameContainsImageLabeller
getContains() - Method in class FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
getContext() - Method in class SharedObjects: Logger and other common configuration
getContext() - Method in class ParametersExperiment
getContext() - Method in class OutputterChecked: General settings for writing outputs.
getContext() - Method in class InputProcessContext
getContextExperiment() - Method in class InputBound: The input-output context associated with the current experiment.
getContextJob() - Method in class InputBound: The input-output context associated with the current job.
getConvert() - Method in class ConvertWithHistogram
getConverters() - Method in class DisplayStack
getCopyFilesNaming() - Method in class CopyFilesNamingOne
getCost(int, int) - Method in class CostMatrix: Gets the cost from an element from the first-list to an element from the second-list.
getCost() - Method in class MergeStrategy: A cost of how undesirable (the higher the more undesirable) this merge is.
getCosts() - Method in class AssignmentObjectFactory
getCount() - Method in class Counter
getCount() - Method in class RunningSum: The running count
getCount(int) - Method in class Histogram
getCount() - Method in class VarianceCalculator
getCountThreshold() - Method in class SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCountXY() - Method in class RunningSumPoint: The count for XY dimensions (guaranteed to always be the same
getCountZ() - Method in class RunningSumPoint: The count for Z dimension (this is identical to RunningSumPoint.getCountXY() if only 3D points have ben added)
getCreateMark() - Method in class PointsFitter
getCsvFeaturesAggregated() - Method in class ResultsWriterOutputNames: The CSV of aggregated feature-results, if enabled.
getCsvFeaturesGroup() - Method in class ResultsWriterOutputNames: The CSV individually written for each group, if enabled.
getCsvFeaturesNonAggregated() - Method in class ResultsWriterOutputNames: The CSV of non-aggregated feature-results
getCsvFilePath() - Method in class FilterCsvColumn
getCsvFilePath() - Method in class FromCSVInput
getCurrent() - Method in class DualState
getCurrent() - Method in class OptimizationStep
getCurrentTemp() - Method in class Geometry
getCustomName() - Method in class Feature: An optional additional name that be associated with the feature (defaults to an empty string)
getDatasetName() - Method in class ExperimentResultsExperimentStructure: The name of the experiment including version suffix
getDatasets() - Method in class QuickMultiDatasetExperiment
getDatasets() - Method in class QuickMultiDatasetStructuredExperiment
getDatasetSpecific() - Method in class QuickMultiDatasetExperiment
getDatasetSpecific() - Method in class QuickMultiDatasetStructuredExperiment
getDatasetSuffix() - Method in class FilePathAppendBase: A suffix appended to the dataset name extracted from the reg exp
getDatasetVersion() - Method in class ExperimentResultsExperimentStructure: A version-suffix appended to the dataset name extracted from the reg exp
getDebugModeParams() - Method in class InputManagerParams
getDebugModeParams() - Method in class InputContextParams: Parameters for debug-mode (only defined if we are in debug mode)
getDecode() - Method in class SegmentObjectsFromTensorFlowModel: Decodes inference output into segmented objects.
getDefault() - Static method in class BinaryValues: Default values to use, if not otherwise specified
getDefault() - Static method in class BinaryValuesByte
getDefaultBeanClass() - Method in class AnchorDefaultBeanFactory: Returns null as Optional is not supported by BeanFactory interface.
getDefaultColors() - Method in class OutputWriteSettings: The default color-scheme used for outputs, if no other scheme is specified.
getDefaultExtension() - Method in interface FileFormat: The default extension to write associated with a particular format.
getDefaultExtension() - Method in enum ImageFileFormat
getDefaultExtension() - Method in enum NonImageFileFormat
getDefaultInstances() - Method in class AnchorDefaultBeanFactory
getDefaultInstances() - Static method in class RegisterBeanFactories
getDefine() - Method in class MarkEvaluator
getDefine() - Method in class DefineOutputter
getDefine() - Method in class Develop: Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
getDefine() - Method in class ExportReportFeaturesFromMulti
getDefine() - Method in class FromObjects
getDefine() - Method in class ExportObjectsAsCroppedImages
getDefine() - Method in class SegmentWithMarkedPointProcess: Adds definitions of stacks/objects etc.
getDelaySizeAtEnd() - Method in class MovieFromSlices
getDelegate() - Method in class RasterGeneratorDelegateToRaster
getDelegate() - Method in class UnsignedByteBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class UnsignedIntBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class UnsignedShortBuffer: The underlying storage buffer, to which calls are delegated with our without conversion.
getDelegate() - Method in class InputFromManagerDelegate
getDelegate() - Method in class BoundMinMax
getDelegate() - Method in class CalculateInputFromDelegate
getDelimiter() - Method in class SubsetRangeIfRequested: Character used to split the name into groups.
getDelimiter() - Method in class LastDirectoryAsPrefix
getDelta() - Method in class Mser
getDeltat() - Method in class AnisotropicDiffusion
getDepth() - Method in class TraversalResult: The depth of directories processed, where 1 = root directory traversed, 2 = root directory + one further level etc.
getDepth() - Method in class ImposeResolution: Physical pixel size of a voxel in z-dimension.
getDerivePath() - Method in class AnnotationMarksComparer
getDerivePath() - Method in class MarksComparer
getDerivePath() - Method in class MaskComparer
getDerivePath() - Method in class ObjectComparer
getDerivePath() - Method in class CollapseFileName
getDerivePath() - Method in class RemoveTrailingDirectory
getDescription() - Method in class OutputtedFile
getDescription() - Method in class ManifestDirectoryDescription
getDescription() - Method in class KernelDescision
getDescription() - Method in class KernelWithIdentifier
getDestination() - Method in class IdentifiablePair
getDestination() - Method in class PairPxlMarkMemo
getDestination() - Method in class DualVoxelizedMarks
getDestination() - Method in class ToPixelized
getDestinationDirectory() - Method in class CopyContext: Destination directory for copying.
getDictionaries() - Method in class DictionaryInitialization: Named-store of Dictionary objects.
getDictionary() - Method in class ParametersAsFeatures
getDictionary() - Method in class FeatureInitialization
getDictionary() - Method in class EnergyStack
getDictionary() - Method in class FeaturesInitialization
getDictionary() - Method in class FeatureEvaluator: Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
getDictionary() - Method in class EnergySchemeCreatorByElement
getDictionary() - Method in class ScaleByParams
getDictionary() - Method in class AssignFromDictionary: The dictionary from which an assignment will occur.
getDictionary() - Method in class ScoreVoxels
getDictionary() - Method in class IfParamEqual
getDictionary() - Method in class DictionaryCondition: The dictionary to provide a value to check.
getDictionary() - Method in class FeatureListProviderLDAClassifier
getDictionary() - Method in class FeatureValueCheckMark
getDictionary() - Method in class DefineOutputterWithEnergy
getDictionary() - Method in class GaussianSampler: The dictionary that parameterizes the Gaussian-distribution that is sampled from.
getDictionary() - Method in class Develop: If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
getDictionary() - Method in class SegmentMarksFromImage: If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
getDimensions() - Method in class ReportFeatureForMarks
getDimensions() - Method in class FromDimensionsBase
getDimensions() - Method in class FromDimensionsBase
getDimensions() - Method in class RepeatSlice: Dimensions to create new mask
getDimensions() - Method in class MergeBase
getDimensions() - Method in class WithDimensionsBase
getDimensions() - Method in class WithOptionalDimensionsBase
getDimensions() - Method in class ToDimensions: The dimensions the source image/entity is desired to be scaled to.
getDimensions() - Method in class FromMarks
getDimensions() - Method in class RequireFeatureRelationThreshold
getDimensions() - Method in class PointsFitterToMark
getDimensionsOptional() - Method in class FeatureInputMark
getDimensionsRequired() - Method in class FeatureInputMark
getDimensionsSourceFallback() - Method in class ToDimensions: Source dimensions used as a fallback, if they are not passed as parameter to ToDimensions.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getDirection() - Method in class ConvertToPhysicalDistance: Direction of the distance being converted, defaults to a unit vector along the X-axis
getDirection() - Method in class FeatureMarkDirection
getDirectionVector() - Method in class LineSegment
getDirectionVector() - Method in class FromUnitValueDistance
getDirectory() - Method in class PathDifference: The directory component of the difference, if it exists.
getDirectory() - Method in class InputArguments: A directory indicating where inputs can be located
getDirectory() - Method in class FilesProviderWithDirectoryString: A directory in which to look for files.
getDirectory() - Method in class FileWithDirectoryInput: A directory that must be a containing directory (at some hierarchical level) of file associated with this input.
getDirectory() - Method in class GlobExtractor.GlobWithDirectory: The directory part of the string, or null if it doesn't exist
getDirectory() - Method in class DualPathPredicates: Only accepts any containing directories where the predicate returns true
getDirectory() - Method in class OutputterTarget
getDirectory() - Method in class DirectoryWithPrefix
getDirectory() - Method in class HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectory
getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectoryString
getDirectoryAsPath(InputContextParams) - Method in class FilesProviderWithDirectoryUnary
getDirectoryAsPath(InputContextParams) - Method in class SingleFile
getDirectoryAsPathEnsureAbsolute(InputContextParams) - Method in class FilesProviderWithDirectory: Like getDirectory as Path but converts any relative path to absolute one
getDirectoryDataset() - Method in class QuickMultiDatasetExperiment
getDirectoryDistance() - Method in class QuickMultiDatasetStructuredExperiment: How many directories to recurse back from the current file to the Experiments/ directory
getDirectoryOutput() - Method in class QuickExperiment
getDistance() - Method in class DistanceIndex
getDistance() - Method in class DistanceIndexTwice
getDistance() - Method in class LevelPerObjectNeighbors: How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
getDistanceMapProvider() - Method in class MergeSpatialClusters: A distance map which can also be used for making decisions on merging
getDistanceMax() - Method in class CalculateLevel
getDistanceTransformMultiplyBy() - Method in class AddDistanceTransform: Multiplies the distance transform by this factor to make it more meaningful in a short
getDistanceTransformSmoothSigmaMeters() - Method in class AddDistanceTransform: If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
getDistanceX() - Method in class ReflectInAxesWithinDistance
getDistanceY() - Method in class ReflectInAxesWithinDistance
getDistanceZ() - Method in class ReflectInAxesWithinDistance
getDistanceZEndIfEmpty() - Method in class XYOrientationExtendToZ
getDivideByZeroValue() - Method in class Divide
getDivisor() - Method in class PermutePropertySequenceDouble: Divide by
getDivisor() - Method in class IdentifierModulo: What the identifier is divided by to find the modulo.
getDoubleOrNull(int) - Method in class ResultsVector
getDrawObject() - Method in class SimpleOverlayWriter
getDrawObject() - Method in class DrawOverlay
getDscr() - Method in exception AnchorCombinableException
getDscr() - Method in class ResolvedBound
getDualStack() - Method in class OptimizationContext
getEigenvalue() - Method in class EigenvalueAndVector
getEigenvector() - Method in class EigenvalueAndVector
getElemAllAsFeatureList() - Method in class EnergyScheme
getElemAllCreator() - Method in class EnergySchemeCreatorByElement
getElemByCliqueSize(int) - Method in class EnergyScheme
getElement() - Method in class LabelledWithConfidence
getElement() - Method in class WithConfidence
getElemIndAsFeatureList() - Method in class EnergyScheme
getElemIndCreator() - Method in class EnergySchemeCreatorByElement
getElemPairAsFeatureList() - Method in class EnergyScheme
getElemPairCreator() - Method in class EnergySchemeCreatorByElement
getEllipseSum(double, double, DoubleMatrix2D) - Static method in class Ellipse
getEllipsoidCalculator() - Method in class Ellipsoid
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class Ellipsoid
getElseName() - Method in class FileNamerContext: A fallback name, if a failure occurs when naming.
getEmptyValue() - Method in class CenterOfGravity
getEmptyValue() - Method in class Intersection
getEmptyValue() - Method in class ArbitraryInsidePoint
getEmptyValue() - Method in class IntensityMeanMaxSlice
getEmptyValue() - Method in class IntensityMeanShellBase
getEmptyValue() - Method in class DerivedObject
getEnd() - Method in class SequenceInteger: An index beyond which we cannot iterate (inclusive)
getEndIndex() - Method in class IndexRange: The index if the last element to use in the subsetting range, inclusive.
getEndPoint() - Method in class LineSegment
getEnergy() - Method in class Aggregator
getEnergyChannelIndex() - Method in class Identity
getEnergyChannelIndex() - Method in class RejectIfIntensityLessThan
getEnergyChannelIndex() - Method in class SingleChannel
getEnergyChannelIndex() - Method in class QuantileAcrossConnectedComponents
getEnergyChannelIndexCheck() - Method in class IdentityImposeValueRelationToHistogram
getEnergyChannelIndexFail() - Method in class IdentityImposeValueRelationToHistogram
getEnergyIndex() - Method in class NumberNeighboringVoxels: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class SpecificEnergyChannelBase: Index of which channel in the energy-stack to select
getEnergyIndex() - Method in class FeatureEnergyChannel: Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
getEnergyIndex() - Method in class OutsideRange
getEnergyIndex() - Method in class Intensity: The channel that that forms the histogram
getEnergyIndex() - Method in class AsObjectMask: The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
getEnergyIndex() - Method in class OverlapMaskBase
getEnergyIndexGradient() - Method in class TextureScore
getEnergyIndexMask() - Method in class IntensityMeanShellBase: A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
getEnergyIndexMask() - Method in class Intensity: Optionally, index of another channel that masks the histogram.
getEnergyIndexX() - Method in class IntensityGradientBase
getEnergyIndexY() - Method in class IntensityGradientBase
getEnergyIndexZ() - Method in class IntensityGradientBase
getEnergyScheme() - Method in class MarksWithEnergyBreakdown
getEnergyScheme() - Method in class MarksWithTotalEnergy: Associated Energy Scheme, which should include the EnergySavedPairs
getEnergyScheme() - Method in class VoxelizedMarksWithEnergy
getEnergyScheme() - Method in class EnergySchemeWithSharedFeatures
getEnergyScheme() - Method in class KernelCalculationContext
getEnergyScheme() - Method in class OptimizationContext
getEnergySchemeCreator() - Method in class MarkEvaluator
getEnergySchemeCreator() - Method in class SegmentWithMarkedPointProcess: Creates an energy scheme that assigns an energy score to each collection of marks.
getEnergyStack() - Method in class FeatureInitialization
getEnergyStack() - Method in class ProposerContext
getEnergyStack() - Method in class DualStack: The energy-stack
getEnergyStack() - Method in class FeatureCalculatorFromProvider
getEnergyStack() - Method in class InitializationWithEnergyStack
getEnergyStackOptional() - Method in class FeatureInputEnergy: Returns the energy-stack which may or not be present
getEnergyStackRequired() - Method in class FeatureInputEnergy: Returns the energy-stack or throws an exception if it's not set as it's required.
getEnergyTotal() - Method in class EnergyPair
getEnergyTotal() - Method in class MarksWithEnergyBreakdown
getEnergyTotal() - Method in class MarksWithTotalEnergy: The pre-annealed total energy
getEnergyTotal() - Method in class VoxelizedMarksWithEnergy
getEnergyTotal() - Method in class EnergySavedAll
getEnergyTotal() - Method in class EnergySavedInd
getEnergyTotal() - Method in class EnergySavedPairs: Pairwise energy total
getEquals() - Method in class FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
getErrorMessage() - Method in class ErrorNodeImpl
getErrorNode() - Method in class ProposerContext
getErrorReporter() - Method in interface InputOutputContext: The associated error reporter.
getErrorReporter() - Method in class Outputter
getErrorReporter() - Method in class GraphLogger
getErrorTree() - Method in class ProposerFailureDescription
getExactDepth() - Method in class DirectoryDepth
getException() - Method in exception CheckedStream.ConvertedToRuntimeException
getException(String) - Method in interface NamedProvider: Retrieves the item if it exists, or throws an exception if it doesn't exist.
getException(String) - Method in class LazyEvaluationStore
getException(int) - Method in class ResultsVector
getException(String) - Method in class SharedFeatureSet
getException(String) - Method in class NamedEntries
getExecutionTime() - Method in class KernelDescision
getExecutionTime() - Method in class Reporting
getExperiment() - Method in class ExperimentResultsExperimentStructure
getExperiment() - Method in class ExperimentStructure
getExperimentalManifest() - Method in class ParametersExperiment
getExperimentArguments() - Method in class InputOutputContextStateful
getExperimentArguments() - Method in class ParametersExperiment
getExperimentDescription() - Method in class OptimizationContext
getExperimentIdentifier() - Method in class OutputExperiment: A name for the experiment.
getExperimentIdentifier() - Method in class ParametersExperiment
getExperimentManifest() - Method in class CoupledManifests
getExperimentType() - Method in class FilePathAppendBase: A folder identifying the type of experiment (where the outputs are all put in the same directory
getExperimentType() - Method in class QuickMultiDatasetStructuredExperiment: The value of $1 (see comment above) in naming-structure.
getExperimentType() - Method in class RootedExperiment: A directory identifying the type of experiment.
getExpression() - Method in class RegExSimple: A Java-style regular expression containing groups.
getExpression() - Method in class MatchRegularExpression
getExpression() - Method in class RegularExpression
getExtension() - Method in class FilenameSplitExtension: The extension of the filename.
getExtension() - Method in class OneOrThreeChannelsWriter
getExtension() - Method in class AppendStack
getExtension() - Method in class AppendStackDirect
getExtensions() - Method in class MatchExtensions: A set of file-extensions (without the period), one of which must match the end of a path.
getExtensions() - Method in class BranchExtension: Any extensions to match (case insensitive) not including any leading period.
getExtent() - Method in class KernelPointCursor
getExtractScoreSize() - Method in class DirectAssignMode
getExtractScoreSize() - Method in class UniformProposal
getExtractScoreSizeReport() - Method in class TransformationAssignMode
getExtractScoreSizeState() - Method in class TransformationAssignMode
getExtractWeight() - Method in class KernelInitialMarksFromPartition
getExtraLength() - Method in class Midpoint
getFactor() - Method in class ScoreObjects
getFactor() - Method in class Scale
getFactorHigh() - Method in class Identity
getFactorLow() - Method in class Identity
getFactorStandardDeviation() - Method in class GaussianSampler: Multiples the standard deviation of the distribution found in keyStandardDeviation.
getFallback() - Method in class SpecificPathList: If no paths can be found either from listPaths or the input-context, then the fallback is called if exists, otherwise an error is thrown
getFallback() - Method in class ToSuggested: Used as a delegate to calculate the scale if suggestedResize is empty when passed to ToSuggested.calculate(java.util.Optional<org.anchoranalysis.image.core.dimensions.Dimensions>, java.util.Optional<org.anchoranalysis.image.core.dimensions.size.suggestion.ImageSizeSuggestion>).
getFallback() - Method in class RGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallbackName() - Method in class ExperimentIdentifierAuto: If there's no task-name, then this constant is used as a fallback name
getFeature() - Method in class ListSequence: The list feature that is duplicated, and populated.
getFeature() - Method in class FeatureProviderDefine
getFeature() - Method in class FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session.
getFeature() - Method in class OutputFeatureTable: A list of features to calculate in an evaluation context.
getFeature() - Method in class ScoreObjects: Feature that calculates the score for an object.
getFeature() - Method in class PermuteFeatureBase
getFeature() - Method in class AddCriteriaFeatureRelationThreshold
getFeature() - Method in class FeatureValueCheckMark
getFeature() - Method in class RequireFeatureRelationThreshold
getFeatureCondition() - Method in class IfCondition
getFeatureCondition() - Method in class IfConditionWithinRange: Calculates value for the condition - which is checked if it lies within a certain range
getFeatureElse() - Method in class IfCondition
getFeatureEvaluator() - Method in class MultipleComparer
getFeatureEvaluator() - Method in class ReportFeatureEvaluator
getFeatureEvaluator() - Method in class FeatureCostAssigner
getFeatureEvaluator() - Method in class DiscardOutliers
getFeatureEvaluator() - Method in class RelationWithMatches
getFeatureEvaluator() - Method in class ThresholdedFeature
getFeatureEvaluator() - Method in class ObjectCollectionProviderWithFeature
getFeatureEvaluator() - Method in class MergeGreedyToIncreaseObjectFeature
getFeatureEvaluator() - Method in class MergeToIncreaseObjectFeature
getFeatureEvaluatorMatch() - Method in class RelationWithMatches
getFeatureEvaluatorMerge() - Method in class MergePairs
getFeatureEvaluatorThreshold() - Method in class MergePairs: Allows merge only if the feature-value satisfies a relation to this threshold
getFeatureListRef() - Method in class FeatureProviderReference
getFeatureListSet() - Method in class FeaturesInitialization
getFeatureNameIndex() - Method in class FeatureInputResults
getFeatureNames() - Method in class InputProcessContext
getFeatureNames() - Method in class SharedStateExportFeatures
getFeatureProvider() - Method in class FeatureEvaluator: The single feature that will be calculated (possibly repeatedly) in the session
getFeatures() - Method in class FeatureListEvaluator: A list of providers, combined together to form a list of features, to be calculated in a session
getFeatures() - Method in class ExportFeatures: The features to be exported (after possibly some manipulation or augmentation)
getFeatures() - Method in class SegmentInstanceWithModel: Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class ExportFeatures: Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
getFeaturesImage() - Method in class PairNeighbors: Additional features that only depend on the image, so do not need to be replicated for every object.
getFeaturesPair() - Method in class PairNeighbors: Additional features that are processed on the pair of images (i.e.
getFeatureTables() - Method in class Develop: Specifies a feature-table that can also be outputted.
getFeedbackReceiver() - Method in class FeedbackReceiverRequireArguments
getFeedbackReceiver() - Method in class SegmentWithMarkedPointProcess: Processes feedback from the segmentation algorithm for outputting / debugging.
getFile() - Method in class NamedChannelsInputPart
getFile() - Method in class NamedFile: The file.
getFile() - Method in class SingleFileInputBase
getFile() - Method in class DualPathPredicates: Only accepts files where the predicate returns true
getFileExtension() - Method in class FileType
getFileFilter() - Method in class ExperimentResultsExperimentStructure: Files to search for
getFileId() - Method in class AppendCsv: Unique identifier for the stack, object-mask-collection etc.
getFileId() - Method in class FilePathBaseAppendToManagerWithFileID: Unique identifier for the stack, object-mask-collection etc.
getFileInput() - Method in class GroupFiles
getFileInput() - Method in class NamedChannels
getFileInput() - Method in class Stacks
getFileInput() - Method in class QuickExperiment: A string indicating the input file(s)
getFilename() - Method in class PathDifference: The file-name component of the difference, if it exists.
getFileName() - Method in class OutputtedFile
getFileName() - Method in class ReportFeatureForManifestFileBase
getFilePath() - Method in class SortedSetSlice
getFilePath() - Method in class FromSerializedMarks
getFilePath() - Method in class FromSerializedObject
getFilePathParser() - Method in class MultiFileReader
getFilePathProviderSVM() - Method in class FeatureListProviderSVMClassifier
getFilePaths() - Method in class FilePathInitialization: Named-store of file-paths.
getFilePaths() - Method in class FeaturesInitialization
getFilePrefix() - Method in class MovieFromSlices
getFiles() - Method in class TraversalResult: All files in any directories that have been traversed.
getFiles() - Method in class ReadFromFile: Provides a single file containing a dictionary.
getFiles() - Method in class FilesProviderUnary
getFiles() - Method in class FilesProviderWithDirectoryUnary
getFiles() - Method in class FromFiles: A provider that should return exactly one File whose path is employed.
getFiles() - Method in class Rooted
getFiles() - Method in class NamedFiles: The files to use as inputs.
getFiles() - Method in class NamedFilesWithDirectory: The files to use as inputs.
getFiles() - Method in class QuickBase: A path to the main channel of each file
getFilter() - Method in class IfObjectFilter
getFilter() - Method in class ObjectCollectionProviderFilterBase
getFilter() - Method in class Filter
getFilter() - Method in class ImageLabellerStringMap
getFilterExtensions() - Method in class InputArguments: If defined, a set of extension filters that can be applied on inputDirectory
getFilterFilesCsv() - Method in class QuickBase: If set, a CSV is read with two columns: the names of images and a
getFilterGlob() - Method in class InputArguments: If defined, a glob that is applied on inputDirectory
getFilterInitialization(Path) - Method in class SharedStateFilteredImageOutput
getFindOutlinePixelAngle() - Method in class TraversePointsOnContour
getFirst() - Method in class CostMatrix
getFirst() - Method in class FeatureInputPairObjects
getFirst() - Method in class OutputEnableRulesSpecify: Output-names in the first-level.
getFirst() - Method in class Compose: First transformation from S to U
getFirst() - Method in class PrecalculationOverlay
getFirstArgument() - Method in class HelpConfig: What the application argument is described as in the help message e.g. experimentFile.xml
getFirstBinaryValues() - Method in class ObjectCollection
getFirstBinaryValuesByte() - Method in class ObjectCollection
getFirstDimensions() - Method in class StackNotUniformSized
getFirstExtent() - Method in class VoxelsWrapperList
getFirstPoint() - Method in class Contour
getFloat() - Static method in class VoxelsFactory
getFontColor() - Method in class TextStyle: Font-color of drawn text
getFontName() - Method in class TextStyle: Font-name of drawn text
getFontSize() - Method in class TextStyle: Font-size of drawn text
getForAllSlices(int) - Method in class IndexByRegion
getForceReader() - Method in class BioformatsReader: If non-empty forces usage of a particular bioformats plugin
GetForSeries<T,S> - Interface in org.anchoranalysis.plot
getForSlice(int, int) - Method in class IndexByRegion
getFoundDirectory() - Method in class FinderSingleDirectory
getFoundFile() - Method in class FinderSingleFile
getFoundOrLog(String, Logger) - Method in interface Findable: Returns the found object (or empty() if it's not found.....
getFoundOrLog(String, Logger) - Method in class Found
getFoundOrLog(String, Logger) - Method in class NotFound
getFriendlyName() - Method in class Feature
getFriendlyName() - Method in interface InitializableFeature: A friendly name that can be displayed to user describing the Feature.
getFrom() - Method in class TypedEdge: The vertex the edge joins from.
getFunction() - Method in class ManifestDescription: Identifies the function the entity plays.
getGaussianSigmaMeters() - Method in class AddEdgeFilters
getGenerator() - Method in class BoundOutputter: The generator to be (repeatedly) used to write elements in the sequence.
getGeneratorList() - Method in class CombineRasterGenerator
getGlob() - Method in class MatchGlob: The string describing a glob e.g.
getGlob() - Method in class GlobExtractor.GlobWithDirectory
getGradient() - Method in class ScoreVoxels
getGraphColorScheme() - Method in class PlotIndexBase
getGrayscaleReconstruction() - Method in class MinimaImpositionGrayscaleReconstruction
getGreen() - Method in class RGBColorBean
getGreen() - Method in class RGBColor
getGreen() - Method in class ThreeChannels
getGroup() - Method in class RowLabels: an identifier for a higher-level group which the row belongs to (foreign key)
getGroup() - Method in class AnnotationLabel: Specifies a group for the label (similar labels that are displayed together)
getGroup() - Method in class ExportFeatures: If non-null this file-path is used to determine the group of the file If null, no group is included.
getGroup() - Method in class GroupedStackBase: If defined, translates a file-path into a group.
getGroup() - Method in class CSVRow
getGroup() - Method in class AppendHistogram
getGroupGeneratorName() - Method in class InputProcessContext
getGroupHeaders() - Method in class LabelHeaders: Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
getGroupMap() - Method in class GroupedSharedState
getGroupNum() - Method in class RootFilePathRegEx
getHeaders() - Method in class FeatureCSVMetadata: Headers for the CSV file
getHeaders() - Method in class CSVReader.OpenedCSVFile
getHeight() - Method in class SizeXY: Size in Y dimension.
getHeight() - Method in class ImposeResolution: Physical pixel size of a voxel in y-dimension.
getHistogram() - Method in class HistogramProviderUnary
getHistogram() - Method in class FeatureInputHistogram
getHistogram() - Method in class ConvertWithHistogram: If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
getHistogram() - Method in class SegmentChannel: An optional histogram of voxel intensity values which can be used by segment
getHistogram() - Method in class PlotHistogram: The histogram to plot.
getHistogram() - Method in class LevelResult
getHistogram() - Method in class FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getHistogramChannelIndex() - Method in class CalculateLevelBase
getHistogramIndex() - Method in class IdentityImposeValueRelationToHistogram
getHistogramsExtra() - Method in class ScoreVoxels
getHorizontalAlign() - Method in class Overlay
getId() - Method in class DictionaryProviderReference
getId() - Method in class Reference
getId() - Method in class FeatureProviderReference
getId() - Method in class StatisticForFeature
getId() - Method in class BinarySegmentationReference
getId() - Method in class FilePathProviderReference
getId() - Method in class KernelDescision
getId() - Method in class Reference
getId() - Method in class FromChannel
getId() - Method in class Reference
getId() - Method in class Reference
getId() - Method in class Reference
getId() - Method in class ReferenceOrElse
getId() - Method in class Reference
getId() - Method in class FeatureIntersectingObjects: ID for the particular object-collection
getId() - Method in class ExportFeatures: Translates an input file name to a unique ID
getId() - Method in class MarkBoundsReference
getId() - Method in class MarkProposerReference
getId() - Method in class MarkMergeProposerReference
getId() - Method in class MarkSplitProposerReference
getId() - Method in class Reference
getId() - Method in class ReferenceOrEmpty
getId() - Method in class CreateEllipse
getId() - Method in class CSVRow
getId() - Method in class Reference
getIdentifier(T, int) - Method in interface IdentifierGetter
getIdentifier(T, int) - Method in class IdentifierModulo
getIdentifier(T, int) - Method in class IdentifyByIteration
getIdentifier(ObjectWithProperties, int) - Method in class IdentifierByProperty
getIdentifier() - Method in class NamedFile: Unique identifier associated with the file.
getIdentifier(Mark, int) - Method in class IdentifierFromMark
getIdentifier() - Method in class Mark
getIdentifier() - Method in class OverlayMark
getIdentifier() - Method in class KernelWithIdentifier
getIdentifier() - Method in interface Identifiable
getIdentifier(Overlay, int) - Method in class IdentifierFromOverlay
getIdentifier(ObjectWithProperties, int) - Method in class IdentifyDelegateToOverlays
getIdentifier() - Method in class OverlayObjectMask
getIdentifierSubrange() - Method in class InputArguments: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIdentifierSubrange() - Method in class InputContextParams: If defined, this indicates and specifies only a subset of the naming-elements to use.
getIdentifierSuffix() - Method in class QuickMultiDatasetExperiment
getIdentifierSuffix() - Method in class QuickMultiDatasetStructuredExperiment
getIdGenerator() - Method in class ExportObjectsFromCSV
getIdGetter() - Method in class IdentifierModulo
getIdGetter() - Method in class ObjectDrawAttributes: Gets a unique ID associated with the object
getIfPresent(K) - Method in class LRUCache: Gets an value if present, but doesn't create any new entry if it's absent.
getIgnoreContains() - Method in class AnnotationBackground: If non-empty any stackNames (after map) containing a certain string will be ignored
getImage() - Method in class MergedPairsFeatures
getImage() - Method in class PointsInitialization
getImage() - Method in class InitializationWithEnergyStack
getImageDimensions() - Method in class ImageFileShape
getImageLabeller() - Method in class ImageAssignLabel: Maps a label to an image
getImgChannelMapCreator() - Method in class GroupFiles
getIncrement() - Method in class SequenceInteger: Size of step to use when incrementing
getIndex() - Method in class Indexable
getIndex() - Method in interface IndexGetter
getIndex(String) - Method in class NamedFeatureStore
getIndex() - Method in class DistanceIndex
getIndex() - Method in class ChannelEntry
getIndex() - Method in class KernelPointCursor
getIndex() - Method in class OutputtedFile
getIndex(TreeNode) - Method in class ErrorNodeImpl
getIndex() - Method in class KernelDescision
getIndex() - Method in class AtIndex
getIndex() - Method in class SliceAt: Index in z-dimension of slice to extract
getIndex() - Method in class SpecificAxisBase: Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
getIndex() - Method in class IndexedRegionBase
getIndex() - Method in class OrderedRadius
getIndex() - Method in class AsObject
getIndex() - Method in class HOGFeature: Which index to return from the HOG descriptor
getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class FromCSVSharedState
getIndexEnd() - Method in class ExtractSliceRange: Slice index to end extracting from (inclusive).
getIndexForMemo(VoxelizedMarkMemo) - Method in class EnergyMemoList
getIndexHighest() - Method in class DistanceIndexTwice: Highest-level index.
getIndexLowest() - Method in class DistanceIndexTwice: Lowest-level index.
getIndexNonZero() - Method in class SelectSlicesWithIndexBase
getIndexStart() - Method in class ExtractSliceRange: Slice index to start extracting from (inclusive).
getIndividual() - Method in class MarksWithEnergyBreakdown
getInitContext() - Method in class FeedbackBeginParameters
getInitialization() - Method in class InitializableBean
getInitialization() - Method in class ImageLabellerStringMapInitialization
getInitialKernel() - Method in class KernelProposer
getInitialPoint() - Method in class ContiguousVoxelPath
getInitParamType() - Method in class PropertyInitializer
getInnerCoreDistance() - Method in class Ellipsoid
getInput() - Method in class AnnotationInputManager
getInput() - Method in class InputOutputExperiment: The input-manager to specify where/which/how necessary inputs for the experiment occur.
getInput() - Method in class InputBound
getInput() - Method in class ParametersUnbound
getInput() - Method in class InputManagerUnary
getInput() - Method in class ExperimentExecutor
getInput() - Method in class MultiInputManager
getInput() - Method in class AnnotationComparisonInputManager
getInput() - Method in class AnnotationComparisonInput
getInput() - Method in class NamedChannelsAppend
getInput() - Method in class Exclude
getInput() - Method in class ConvertNamedChannelsToStack
getInput() - Method in class FromCSVInputManager
getInputContext() - Method in class InputManagerParams
getInputDebug() - Method in class BranchIfDebug
getInputDirectory() - Method in class FileNamerContext: A directory associated with the inputs, which if defined, is guaranteed to be a parent of them all.
getInputDirectory() - Method in class InputContextParams: If defined, a directory which can be used by beans to find input
getInputFilterExtensions() - Method in class InputContextParams: A list of extensions that can be used filter inputs
getInputFilterGlob() - Method in class InputContextParams: A glob that can be used by beans to filter input
getInputIfPresent(T) - Method in class CacheTransferSource
getInputName() - Method in class MultiInputManager
getInputName() - Method in class QuickExperiment
getInputName() - Method in class MultiInputManagerQuick
getInputOutput() - Method in class InitializationContext: The input-output context.
getInputOutputContext() - Method in class OptimizationContext
getInputPaths() - Method in class InputContextParams: A list of paths referring to specific inputs
getInputPointShift() - Method in class ConicFitterBase
getInstance() - Static method in class InterpolatorFactory
getInt(int) - Method in class VoxelBuffer: Gets an element from the buffer at a particular position, converting, if necessary, to an int.
getInt(int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
getInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
getIntensity() - Method in class ScoreVoxels
getIntensityHistogram() - Method in class BinarySegmentationParameters
getIntensityProvider() - Method in class GenerateString
getInterpolator() - Method in class ScaleXY
getInterpolator() - Method in class OutlinePreserveRelativeSize: Interpolator used when scaling the background
getInterpolator() - Method in class ScaleToSize
getItem() - Method in class NamedBean: The item that is to be named (i.e.
getItem() - Method in class SingleContainer
getItem() - Method in class DefineSingle
getItem() - Method in class PrependName
getItem() - Method in class FeatureUnary
getItem() - Method in class FeatureDeriveFromPair
getItem() - Method in class ReportFeatureWrapError
getItem() - Method in class ThresholdHistogram
getItem() - Method in class DeriveFromPair
getItem() - Method in class FeatureListProviderAggregatePair: For each feature in the list, a corresponding "aggregate" feature is created in the output list
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class DerivedObject
getItem() - Method in class FeatureIntersectingObjectsSingleElement
getItem() - Method in class PairedWithMask
getItem() - Method in class RejectIfIntensityLessThan
getItem() - Method in class FeatureSingleObjectFromShared
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class AsObjectMask
getItem() - Method in class QuantileAcrossConnectedComponents
getItem() - Method in class Rooted
getItem() - Method in class CoefficientOfVarianceFromAll
getItem() - Method in class MeanFromAll
getItem() - Method in class Intensity: Feature to apply to the histogram
getItem() - Method in class FeaturePairMemoOne
getItem1() - Method in class FeatureDoubleElem
getItem2() - Method in class FeatureDoubleElem
getItemMean() - Method in class StatisticalBase
getItemProportionate() - Method in class FeatureAsIndividualProportionate
getItemStdDev() - Method in class StatisticalBase
getIteration() - Method in class Reporting
getIterations() - Method in class AnisotropicDiffusion
getIterations() - Method in class MorphologicalOperatorBase
getIterations() - Method in class ObjectCollectionProviderMorphological
getIterations() - Method in class Repeat: The maximum number of iterations.
getIterations() - Method in class Intersection: The number of dilations and erosions to apply to determine if two objects intersect
getIterations() - Method in class IntensityMeanShellBase: The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class Erode
getIterations() - Method in class NumberRemovedVoxelsAfterClosing
getIterations() - Method in class Shell: The number of dilations and erosions to apply and whether to do in the Z dimension
getIterations() - Method in class MorphologicalOperation: iterations for erode, dilate, open, close
getIterations() - Method in class UniformProposal
getIterations() - Method in class NumberIterationsBase: The number of iterations for which the number-of-marks must remain constant.
getIterationsDilation() - Method in class MorphologicalIterations: Number of times to perform morphological dilation
getIterationsErosion() - Method in class MorphologicalIterations: Number of times to perform morphological erosion
getJobDescription() - Method in class SubmittedJob
getJobManifest() - Method in class CoupledManifests
getJobNumber() - Method in class JobDescription
getJobShortName() - Method in class JobDescription
getJobState() - Method in class SubmittedJob
getKappa() - Method in class AnisotropicDiffusion
getKeep() - Method in class MergeCandidate
getKeepProcessorsFree() - Method in class DebugDependentProcessor: How many processors to avoid using for the tasks.
getKeepProcessorsFree() - Method in class ParallelProcessor: How many processors to avoid using for the tasks.
getKernel() - Method in class KernelWithIdentifier
getKernel() - Method in class WeightedKernel
getKernel() - Method in class OptimizationStep
getKernel() - Method in class Reporting
getKernel() - Method in class KernelProposerOptionSingle
getKernelAccepted() - Method in class Aggregator
getKernelApplication() - Method in class DilationContext: How the kernel is applied to the scene.
getKernelCalcContext() - Method in class TransformationContext
getKernelFactoryList() - Method in class FeedbackBeginParameters
getKernelHalfWidth() - Method in class Median: Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
getKernelNegative() - Method in class KernelProposerOptionDual
getKernelNoProposalDescription() - Method in class Reporting
getKernelPositive() - Method in class KernelProposerOptionDual
getKernelProposed() - Method in class Aggregator
getKernelProposer() - Method in class SegmentWithMarkedPointProcess: Proposes kernel-changes during iterations of hte marked-point-processes.
getKernelStateBridge() - Method in class TransformationAssignMode
getKey() - Method in exception GetOperationFailedException
getKey() - Method in class AssignFromDictionary: The key of the value in the dictionary that will be assigned.
getKey() - Method in class IfParamEqual
getKey() - Method in class DictionaryCondition: The key in the dictionary whose value is checked.
getKey() - Method in class ParamFromCollection
getKey() - Method in class FilePathParser
getKey() - Method in class RegularExpression
getKey() - Method in class FromDictionary
getKeyGroupID() - Method in class RegularExpression
getKeyLower() - Method in class ScaleByParams
getKeyMean() - Method in class GaussianSampler: The name of the key in the dictionary with the mean of the distribution.
getKeyPrefix() - Method in class FromDictionary: Prefix prepended to key
getKeyStandardDeviation() - Method in class GaussianSampler: The name of the key in the dictionary with the standard-deviation.
getKeySuffix() - Method in class FromDictionary
getKeyUpper() - Method in class ScaleByParams
getLabel() - Method in class ImageLabelAnnotation: The label that applies to the image
getLabel() - Method in class StackProviderWithLabel
getLabel() - Method in class LabelledWithConfidence: The label associated with the element.
getLabelMap() - Method in class ImageCSVLabellerInitialization
getLabels() - Method in class PlotIndexBase
getLabels() - Method in class WholeImageLabelStrategy
getLastDivider() - Method in class Aggregator
getLastPoint() - Method in class Contour
getLastPoints1() - Method in class MarkMergeProposer
getLastPoints2() - Method in class MarkMergeProposer
getLeafDirectories() - Method in class TraversalResult: All the directories in the bottom-most depth that was traversed.These directories were not traversed
getLeft() - Method in class ObjectsToCompare: Objects on left-side of the comparison
getLevel() - Method in class Constant
getLevel() - Method in class LevelResult
getLine() - Method in class CSVRow
getList() - Method in class Concatenate
getList(Class<?>) - Method in class Define
getList() - Method in class RegExList
getList() - Method in class StringMap
getList() - Method in class ToMultiple: The list of loggers to log to
getList() - Method in class MessageLoggerList
getList() - Method in class Define
getList() - Method in class DefinedNamed
getList() - Method in class FeatureList
getList() - Method in class FeatureListElem
getList() - Method in class ArrangeRaster
getList() - Method in class Combine
getList() - Method in class TileWithLabels
getList() - Method in class FinderExperimentFileDirectories
getList() - Method in class RegionMap
getList() - Method in class AddCriteriaOr
getList() - Method in class FeedbackReceiverList
getList() - Method in class TerminationConditionListOr
getList() - Method in class Concatenate
getList() - Method in class CalculateLevelListBase
getList() - Method in class ObjectFilterCombine: A list of other filters from which the sub-classes implement filtering behaviour.
getList() - Method in class Concatenate
getList() - Method in class Sequence: A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
getList() - Method in class Concatenate
getList() - Method in class SpecificAndRename
getList() - Method in class FromEntries
getList() - Method in class Combine
getList() - Method in class Concatenate
getList() - Method in class SummarizerAggregate
getList() - Method in class AndList
getList() - Method in class VisitSchedulerAnd
getList() - Method in class VisitSchedulerUniformSample
getList() - Method in class MarkProposerFromList
getListAdditionalChannelProviders() - Method in class ScoreObjects
getListAppend() - Method in class NamedChannelsAppend
getListAppend() - Method in class MultiInputManagerQuick: Additional entities that are appended to the multi-input
getListComparers() - Method in class MultipleComparer
getListFeatures() - Method in class BinaryClassifierImageLabeller
getListFromManager(MultiInputManager) - Method in class AppendDictionary
getListFromManager(MultiInputManager) - Method in class AppendFilePath
getListFromManager(MultiInputManager) - Method in class AppendHistogram
getListFromManager(MultiInputManager) - Method in class AppendMarks
getListFromManager(MultiInputManager) - Method in class AppendObjects
getListFromManager(MultiInputManager) - Method in class AppendStack
getListFromManager(MultiInputManager) - Method in class AppendStackDirect
getListFromManager(MultiInputManager) - Method in class FilePathBaseAppendToManager
getListImageFeatures() - Method in class EnergySchemeCreatorByElement
getListImageFeatures() - Method in class EnergyScheme
getListPaired(boolean) - Method in interface Assignment
getListPaired(boolean) - Method in class AssignmentMaskIntersection
getListPaired(boolean) - Method in class AssignmentOverlapFromPairs
getListPaths() - Method in class SpecificPathList: If specified, this forms the list of paths which is provided as input.
getListReportFeatures() - Method in class ExportReportFeatures
getListStackProvider() - Method in class ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getListStackProviderMIP() - Method in class ExportObjectsAsCroppedImages: The channels we extract the object-masks from - all assumed to be of same dimension
getListUnassigned(boolean) - Method in interface Assignment
getListUnassigned(boolean) - Method in class AssignmentMaskIntersection
getListUnassigned(boolean) - Method in class AssignmentOverlapFromPairs
getListUnassignedLeft() - Method in class AssignmentOverlapFromPairs
getListUnassignedRight() - Method in class AssignmentOverlapFromPairs
getLocal(int) - Method in interface BufferRetriever: All local access is indexed relative (e.g.
getLocal(int) - Method in class LocalSlices
getLocalPath() - Method in class AnchorBean: A local path on the filesystem associated with this bean (from serialization) if defined.
getLog() - Method in class OnlyIf: The logger to use if conditions are fulfilled
getLogExperiment() - Method in class OutputExperiment: Where log messages that do not pertain to a specific job (input) appear.
getLogExperimentPath() - Method in class QuickMultiDatasetExperiment: Relative path to a logger for the experiment in gneeral
getLogger() - Method in class InitializableBean: The logger
getLogger() - Method in class CommonContext: The logger
getLogger() - Method in class InitializationContext
getLogger() - Method in class InputBound
getLogger() - Method in class InputOutputContextStateful
getLogger() - Method in class InputManagerParams
getLogger() - Method in class FileNamerContext: Logs information messages.
getLogger() - Method in interface InputOutputContext: The associated logger.
getLogger() - Method in class ReporterAggregate
getLogger() - Method in class FeedbackEndParameters
getLogger() - Method in class OptimizationContext
getLogger() - Method in class TransformationContext
getLogger() - Method in class CalculateFeaturesForObjects
getLogger() - Method in class InputProcessContext
getLoggerExperiment() - Method in class ParametersExperiment
getLoggerTaskCreator() - Method in class ParametersExperiment: This is a means to create new log-reporters for each task.
getLogReporterJob() - Method in class InputBound
getLogTask() - Method in class InputOutputExperiment: Where log messages that do pertain to a specific job (input) appear.
getLogTaskPath() - Method in class QuickMultiDatasetExperiment: Relative path to a logger for a specific task
getMainChannelIndex() - Method in class NamedChannelsQuick: Index of the mainChannel
getMainChannelName() - Method in class NamedChannelsQuick: The name of the channel provided by the rasters in file Provider
getMainObjectName() - Method in class MultiInput
getMainObjectName() - Method in class StackWithMap
getMajorAxisAngle() - Method in class EllipseStandardFormConverter
getMajorAxisSlope() - Method in class EllipseStandardFormConverter
getManifest() - Method in class InputBound
getManifestDescription() - Method in class OutputPattern: A manifest-description for the directory, if defined.
getManifestDescription() - Method in class FileType
getManifestDescriptionFunction() - Method in class MarksGeneratorBase
getManifestDeserializer() - Method in class CoupledManifestsInputManager
getManifestExperimentInputFileSet() - Method in class CoupledManifestsInputManager
getManifestFunction() - Method in class ObjectSerializerPeriodicReporter
getManifestFunction() - Method in class VoxelizedMarksChangeReporter
getManifestInputFileSet() - Method in class CoupledManifestsInputManager
getMap() - Method in class OperationMap
getMap() - Method in class ImageLabellerStringMap
getMap() - Method in class ImageLabellerStringMapInitialization
getMapping() - Method in class AnonymizeSharedState
getMark() - Method in class FeatureInputMark
getMark() - Method in class VoxelizedMarkMemo: The associated mark
getMark() - Method in class OverlayMark
getMark() - Method in class KernelDeath.MarkAnd
getMark() - Method in class ObjectWithEllipse
getMarkBounds() - Method in class MarkBoundsDefine
getMarkBounds() - Method in class SegmentThresholdAboveMinBound
getMarkEvaluator() - Method in class MarkProposerStrategy: A mark-evaluator that is added to the GUI to support this annotation
getMarkFactory() - Method in class MarkEvaluator
getMarkFactory() - Method in class KernelCalculationContext
getMarkFactory() - Method in class MarkFactoryContext
getMarkFactory() - Method in class OptimizationContext
getMarkFactory() - Method in class SegmentWithMarkedPointProcess: Creates a new mark, before perhaps further manipulations by a kernel.
getMarkFactory() - Method in class FitPointsFromObjects
getMarkFromMarksProposer() - Method in class KernelSplit
getMarkProposer() - Method in class MarkProposerStrategy: Name of the MarkProposer to use.
getMarkProposer() - Method in class FromMarkProposer
getMarkProposer() - Method in class MergeMarkEllipse
getMarkProposer() - Method in class MarkEllipseSimple
getMarkProposer() - Method in class KernelBirthAndKill
getMarkProposer() - Method in class KernelExchange
getMarkProposer() - Method in class KernelBirthPixelized
getMarkProposerAdditionalBirth() - Method in class KernelBirthAndKill
getMarkProvider() - Method in class CreateMarkFromPoints
getMarkProvider() - Method in class ReportFeatureOnMark
getMarkProvider() - Method in class FromSingleMark
getMarkProvider() - Method in class RequireFeatureRelationThreshold
getMarkRmv() - Method in class KernelDeath
getMarks() - Method in class RandomCollectionWithAddCriteria
getMarks() - Method in class FeatureInputMarkCollection
getMarks() - Method in class IndexableMarksWithEnergy
getMarks() - Method in class MarksWithEnergyBreakdown
getMarks() - Method in class MarksWithTotalEnergy: The marks
getMarks() - Method in class VoxelizedMarksWithEnergy
getMarks() - Method in class ReportFeatureOnMarks
getMarks() - Method in class MarksWithDisplayStack
getMarks() - Method in class ColoredMarks
getMarks() - Method in class MarkCollection
getMarks() - Method in class FromMarks
getMarks() - Method in class ScaleXY
getMarks() - Method in class RetrieveSingleMarkOnly
getMarks() - Method in class ColoredMarks
getMarks() - Method in class MarksFromPartition
getMarksAfter() - Method in class Reporting
getMarksAfterOptional() - Method in class Reporting
getMarksColored() - Method in class ColoredMarksWithDisplayStack
getMarksProposer() - Method in class KernelInitialMarksFromPartition
getMarksProposer() - Method in class KernelInitialMarksProposed
getMarksProposer() - Method in class KernelInitialMarksVoxelized
getMarksReject() - Method in class DualMarksAnnotation: Marks covering area that should be rejected, can be null
getMarksWithTotalEnergy() - Method in class MarksWithEnergyBreakdown
getMask() - Method in class MaskProviderUnary
getMask() - Method in class FromMaskBase
getMask() - Method in class UnaryWithMaskBase
getMask() - Method in class ScoreVoxels
getMask() - Method in class FromChannel
getMask() - Method in class SegmentChannel: An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
getMask() - Method in class ConnectedComponentsFromMask
getMask() - Method in class AndObjectsWithMasks
getMask() - Method in class FromMask
getMask() - Method in class SegmentChannel
getMask() - Method in class ColoredMask
getMask() - Method in class FromChannelOrMask: A mask that is provided to the stack.
getMask() - Method in class PairedWithMask
getMask() - Method in class MaskAsSingleObject
getMask() - Method in class FillHoles
getMask() - Method in class CheckMarkWithMask
getMask() - Method in class FindPointOnOutlineWalk
getMask() - Method in class XYOrientationExtendToZ
getMaskElse() - Method in class IfPredicateBase: Returned instead of mask if the predicate is not satisfied
getMaskFilled() - Method in class TraverseOutlineOnImage
getMaskFilled() - Method in class XYOrientationExtendToZ
getMaskIndex() - Method in class SurfaceSizeMaskNonZero
getMaskOutline() - Method in class TraverseOutlineOnImage
getMaskValue() - Method in class ExportImageHistograms: What voxel value to read as "On" in the mask above.
getMaskValue() - Method in class OverlapMaskBase
getMatch() - Method in class SelectFromShared
getMatch() - Method in class FilterCsvColumn
getMatch() - Method in class MatchedAppendCsv
getMatcher() - Method in class SearchDirectory
getMatcher() - Method in class MatchExtensions
getMatcher() - Method in class RelationWithMatches
getMatcher() - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
getMatcher() - Method in class Match
getMatches() - Method in class MatchedObject: The matches associated with the source-object
getMatrix() - Method in class CostMatrix: A two-dimensional array mapping the costs from first to second
getMatrix() - Method in class RotationMatrix: The underlying matrix used internally in the rotation-matrix.
getMax() - Method in interface Progress
getMax() - Method in class ProgressConsole
getMax() - Method in class ProgressIgnore
getMax() - Method in class ProgressIncrement
getMax() - Method in class ProgressOneOfMany
getMax() - Method in class BoundMinMax
getMax() - Method in class ResolvedBound
getMax() - Method in class PointListBase
getMax() - Method in class ScaleByMinMaxValue
getMax() - Method in class ClampHistogramMax
getMax() - Method in class UnitsWithinRange: Maximum-boundary for acceptable range
getMax() - Method in class OutsideRange
getMax() - Method in class MaxOverlapRatio
getMax() - Method in class InvertedMax
getMax() - Method in class CompareWithRangeFeature: Calculates maximally-allowed range boundary
getMax() - Method in class RangeCompareFromScalars: Boundary value indicating maximally-allowed range value
getMaxBin() - Method in class Histogram: Maximum bin-value inclusive
getMaxCost() - Method in class MultipleComparer
getMaxCost() - Method in class FeatureCostAssigner
getMaxDirectoryDepth() - Method in class SearchDirectory: If non-negative the max depth of directories.
getMaxDirectoryDepth() - Method in class PathMatchConstraints: Limits on the depth of how many sub-directories are recursed
getMaxDirectoryDepth() - Method in class ExperimentResultsExperimentStructure
getMaxDistance() - Method in class MergeWithOptionalDistanceConstraint: An optional maximum distance
getMaxDistance() - Method in class CostOverlapWithinMidpointDistance
getMaxDistance() - Method in class FindPointOnOutlineWalk
getMaxDistanceBetweenMinima() - Method in class AddDistanceTransform
getMaxDistanceCOG() - Method in class MergeSpatialClusters: The maximum distance allowed between center-of-gravities of objects
getMaxDistanceDeltaContour() - Method in class AddDistanceTransform: The maximum distance allowed between two seeds in terms of their values in the distance map
getMaxDistanceDeltaContour() - Method in class MergeSpatialClusters: The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
getMaxDistanceProposer() - Method in class VisitSchedulerMaxDistanceAlongContour
getMaxDistanceZ() - Method in class XYOrientationExtendToZ
getMaximumIndex() - Method in class BoundedIndexContainerFromList
getMaximumIndex() - Method in interface BoundedRange
getMaximumIndex() - Method in class BoundsFromRange
getMaximumIndex() - Method in class BoundedIndexContainerBridge
getMaximumIndex() - Method in class IntegerSequenceContaner
getMaximumIndex() - Method in class SingleContainer
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class Repeat
getMaxIter() - Method in class RadiiProposerRepeat
getMaxNumberItems() - Method in class Limit
getMaxNumberItems() - Method in class Limit
getMaxNumberProcessors() - Method in class TaskArguments: Suggests a maximum number of processors (CPUs) for a task.
getMaxNumberProcessors() - Method in class DebugDependentProcessor: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class ParallelProcessor: Theoretical maximum number of (CPU) processors to use in parallel.
getMaxNumberProcessors() - Method in class QuickMultiDatasetExperiment: An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
getMaxNumberProcessors() - Method in class QuickMultiDatasetStructuredExperiment
getMaxNumItems() - Method in class LimitWithDirectory
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
getMaxResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
getMaxScaleFactor() - Method in class LargestMultipleWithin: An upper limit on the scale-factor allowed in each dimension.
getMaxSize() - Method in class Mser
getMaxSplitGroups() - Method in class CompareAnnotations
getMaxValue() - Method in class ConsistentChannelChecker
getMaxVar() - Method in class Mser
getMaxVolume() - Method in class FillHoles
getMaxX() - Method in class InsideBoxOn: Maximum X coordinate inclusive
getMaxY() - Method in class InsideBoxOn: Maximum Y coordinate inclusive
getMaxZ() - Method in class InsideBoxOn: Maximum Z coordinate inclusive
getMean() - Method in class FirstSecondOrderStatistic: Mean
getMean(int) - Method in class ImageMoments: Index is the axis (0 for X, 1 for Y, 2 for Z)
getMedianRadiusMeters() - Method in class AddEdgeFilters
getMemoForIndex(int) - Method in class VoxelizedMarksWithEnergy
getMemoForIndex(int) - Method in class EnergyMemoList
getMemoForIndex(int) - Method in class MemoList
getMemoForIndex(int) - Method in interface MemoForIndex
getMemoForMark(Mark) - Method in class VoxelizedMarksWithEnergy
getMemoForMark(MarkCollection, Mark) - Method in class EnergyMemoList
getMemoized() - Method in class FinderSerializedObject: Provides a memoized (cached) means of access the results of the finder
getMerge() - Method in class MergeCandidate
getMerged() - Method in class FeatureInputPairObjects: Returns a merged version of the two-objects available (or null if not available)
getMergedOptional() - Method in class FeatureInputPairObjects
getMergedPosTolerance() - Method in class MergeMarkEllipse
getMergeMarkProposer() - Method in class KernelMerge
getMessage() - Method in exception GetOperationFailedException
getMessage() - Method in class ReportFeatureWrapError
getMessageLogger() - Method in class InputOutputContextStateful: Exposed as StatefulMessageLogger rather than as MessageLogger that is found in Logger
getMessageNoInputs() - Method in class InputOutputExperiment: A message written to the logger if no inputs exist for the experiment, and it thus ends early.
getMessageReporter() - Method in interface InputOutputContext: The associated message reporter.
getMethod() - Method in class AutoLocalThreshold
getMethod() - Method in class ThresholderAutoIJ: One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
getMethod() - Method in class CopyFiles: How the copying occurs from source to destination file.
getMiddlePoint() - Method in class Contour
getMin() - Method in interface Progress
getMin() - Method in class ProgressConsole
getMin() - Method in class ProgressIgnore
getMin() - Method in class ProgressIncrement
getMin() - Method in class ProgressOneOfMany
getMin() - Method in class BoundMinMax
getMin() - Method in class ResolvedBound
getMin() - Method in class PointListBase
getMin() - Method in class ScaleByMinMaxValue
getMin() - Method in class UnitsWithinRange: Minimum-boundary for acceptable range
getMin() - Method in class OutsideRange
getMin(Function<FileDetails, Optional<Integer>>) - Method in class ParsedFilePathBag
getMin() - Method in class RadiiMinRatio
getMin() - Method in class CompareWithRangeFeature: Calculates minimally-allowed range boundary
getMin() - Method in class RangeCompareFromScalars: Boundary value indicating minimally-allowed range value
getMinConfidence() - Method in class ThresholdConfidence: The minimum confidence of an element for its object-mask to be included.
getMinConfidence() - Method in class DecodeMaskRCNN: Only proposals outputted from the model with a score greater or equal to this threshold are considered.
getMinConfidence() - Method in class DecodeText: Proposed bounding boxes below this confidence interval are removed
getMinDiff() - Method in class MeanIntensityDifference
getMinDifference() - Method in class Difference: A minimum difference, below which 0.0 is returned
getMinDifference() - Method in class DifferenceCalculateLevelStandardDeviation
getMinDiversity() - Method in class Mser
getMinimaImposition() - Method in class ImposeMinima
getMinimumBoundingBoxVolume() - Method in class FloodFillEachIntensityLevel: Only objects whose bounding-box volume is greater or equal to this threshold are included.
getMinimumIndex() - Method in class BoundedIndexContainerFromList
getMinimumIndex() - Method in interface BoundedRange
getMinimumIndex() - Method in class BoundsFromRange
getMinimumIndex() - Method in class BoundedIndexContainerBridge
getMinimumIndex() - Method in class IntegerSequenceContaner
getMinimumIndex() - Method in class SingleContainer
getMinimumSize() - Method in class LargestMultipleWithin: The minimum size in each dimension.
getMinIntensity() - Method in class RejectIfIntensityLessThan
getMinIntensity() - Method in class ThresholderSimpleFillHoles2D: Intensity for thresholding
getMinIntensityValue() - Method in class MorphologicalOperatorBase
getMinMaskValue() - Method in class DecodeMaskRCNN: Threshold above which pixels are considered in the mask.
getMinMaxIgnoreBeforeIndex() - Method in class LinePlot
getMinNumberObjects() - Method in class DiscardOutliers
getMinNumberPoints() - Method in class SplitContourAtSaddlePoints: If a contour has less than this number of points, we don't split it, and return it as-is
getMinNumberVoxels() - Method in class SplitIntoSquares: Only includes squares that have at least this number of voxels.
getMinNumberVoxels() - Method in class ConnectedComponentsFromBinarySegmentation
getMinNumberVoxels() - Method in class ThresholdConfidence: The minimum number of voxels that must exist in a connected-component to be included.
getMinNumPoints() - Method in class CreateMarkFromPoints
getMinNumPoints() - Method in class PointsFitterToMark: If an object has fewer points than before being fitted, we ignore
getMinNumSlices() - Method in class XYOrientationExtendToZ
getMinNumZSlices() - Method in class AtLeastZSlices
getMinorAxisAngle() - Method in class EllipseStandardFormConverter
getMinorAxisSlope() - Method in class EllipseStandardFormConverter
getMinOverlap() - Method in class CostOverlapWithinMidpointDistance
getMinRadius() - Method in class LinearLeastSquaresEllipseFitter
getMinRadius() - Method in class LinearLeastSquaresEllipsoidFitter
getMinRadScaleEnd() - Method in class MarkEllipseSimple
getMinRadScaleStart() - Method in class MarkEllipseSimple
getMinRatio() - Method in class DiscardOutliers
getMinResolution() - Method in class MinimumXYResolution
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
getMinResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
getMinResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
getMinSize() - Method in class Mser
getMinusOne() - Method in class SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index -1 or null if it's the first slice.
getMinVal() - Method in class FeatureValueCheckMark
getMinVolume() - Method in class ConnectedComponentsFromMask
getMinVolume() - Method in class VolumeMin
getMinVolumeConnectedComponent() - Method in class AddDistanceTransform
getMinX() - Method in class InsideBoxOn: Minimum X coordinate inclusive
getMinY() - Method in class InsideBoxOn: Minimum Y coordinate inclusive
getMinZ() - Method in class InsideBoxOn: Minimum Z coordinate inclusive
getModelBinaryPath() - Method in class SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb extension, relative to the models/ directory in the Anchor distribution.
getModelDirectory() - Method in class CommonContext: Directory where machine-learning models can be found
getModelDirectory() - Method in class InputArguments
getModelDirectory() - Method in class InputOutputContextStateful
getModelDirectory() - Method in class ImageInitialization
getModelDirectory() - Method in interface InputOutputContext: An input-directory in which models are stored.
getModelDirectory() - Method in class InputProcessContext
getModelPool() - Method in class SharedStateSegmentInstance
getModelTextGraphPath() - Method in class SegmentObjectsFromTensorFlowModel: Relative-path to the TensorFlow model file, likely with .pb.txt extension, relative to the models/ directory in the Anchor distribution.
getMultipleComparer() - Method in class MarkProposerStrategy
getMultiplyBy() - Method in class DistanceTransform3D
getName() - Method in class FromXmlList: The name of the file in the current working directory WITHOUT THE .xml EXTENSION
getName() - Method in class NamedBean: The name associated with item
getName(S) - Method in interface ApplyPermutations.NameGetter
getName() - Method in class RootPath
getName() - Method in interface NameValue: The associated name
getName() - Method in class SimpleNameValue
getName() - Method in class ExperimentIdentifierConstant
getName() - Method in class ChannelEntry
getName() - Method in class OptionalNameValue: An optional-name.
getName() - Method in class IncreasingIntegers
getName() - Method in class IncrementingIntegers
getName() - Method in class SequenceType
getName() - Method in class StringsWithoutOrder
getName() - Method in class NamedPath: A unique name associated with the path
getName() - Method in class Circle
getName() - Method in class Ellipse
getName() - Method in class Ellipsoid
getName() - Method in class Sphere
getName() - Method in class Mark
getName() - Method in class LineSegment
getName() - Method in class PointList
getName() - Method in class Polygon
getName() - Method in class PolygonCurve
getName() - Method in class RotatableBoundingBox
getName() - Method in class Kernel
getName() - Method in class WeightedKernel
getName() - Method in class NamedChannel
getName() - Method in class AdjacentFile: A name to describe the adjacent file
getName() - Method in class FilePathAppendBase: The name of the appended entity
getNameLeft() - Method in class AnnotationComparisonInputManager
getNamer() - Method in class GroupFiles
getNamer() - Method in class RemoveExtension
getNamer() - Method in class SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
getNamer() - Method in class NamedFilesBase
getNamer() - Method in class QuickBase: Assigns each input a unique compact name.
getNameRight() - Method in class AnnotationComparisonInputManager
getNames() - Method in class NamedFeatureCalculatorMulti
getNames() - Method in class AnnotationComparisonInput
getNameSubrange() - Method in class FileNamerContext: If defined, this indicates and specifies only a subset of the naming-elements to use.
getNameValueSet() - Method in class OverlayProperties
getNaming() - Method in class CopyFiles: How an output name (and path) is selected for an input file.
getNamingSharedState() - Method in class RecordingCounter
getNavigateHigherDirs() - Method in class MultiFileReader: Search x number directories higher than file
getNoProposalReason() - Method in class KernelDescision
getNumberBins() - Method in class HOGParameters: The number of bins in each histogram for a cell
getNumberChannels() - Method in class EnergyStack
getNumberChannels() - Method in class EnergyStackWithoutParams
getNumberChannels() - Method in class DisplayStack
getNumberChannels() - Method in class Stack
getNumberChannels() - Method in class StackNotUniformSized
getNumberChannels() - Method in class ScaleableBackground: Number of channels in the stack
getNumberChannels() - Method in class ForceNumberChannels
getNumberChannels() - Method in class ImageFileShape
getNumberColors() - Method in class TiffTimeSeries
getNumberColumns() - Method in class Tile: The number of columns to use in the table produced when tiling.
getNumberConverter() - Method in class AnonymizeSharedState
getNumberDecimalPlaces() - Method in class FeatureCostAssigner
getNumberDigits() - Method in class IncrementingNumber: Number of digits in the number, with leading zeros as necessary.
getNumberDilations() - Method in class LevelPerObjectIndependently
getNumberDimensions() - Method in class RotationMatrix
getNumberElements() - Method in class IncreasingIntegers
getNumberElements() - Method in class IncrementingIntegers
getNumberElements() - Method in class SequenceType
getNumberElements() - Method in class StringsWithoutOrder
getNumberFrames() - Method in class ForceNumberFrames
getNumberFrames() - Method in class ImageFileShape
getNumberGPUProcessors() - Method in class ParallelProcessor: How many GPU processors to use when this is possible as a substitute for a CPU processor
getNumberKernels() - Method in class KernelProposer
getNumberLevelsGrouping() - Method in class CompareAnnotations
getNumberLoopPoints() - Method in class SplitContourAtSaddlePoints
getNumberPoints() - Method in class LinePlot
getNumberRows() - Method in class Tile: The number of rows to use in the table produced when tiling.
getNumberSeries() - Method in class PlotIndexBase
getNumberSlices() - Method in class ImageFileShape
getNumberSubdirectories() - Method in class LastDirectories: How many directories to include in the name.
getNumCols() - Method in class TileWithLabels
getNumColsUsed() - Method in class TableItemArrangement
getNumMarks() - Method in class FromMarkProposer
getNumRowsUsed() - Method in class TableItemArrangement
getObject() - Method in class Found: The found object
getObject() - Method in class FeatureInputSingleObject
getObject() - Method in class OverlayObjectMask
getObject() - Method in class LevelResult
getObject() - Method in class ObjectVertex
getObject() - Method in class ObjectWithEllipse
getObject1() - Method in class FeatureInputPairMemo
getObject2() - Method in class FeatureInputPairMemo
getObjectMatcher() - Method in class Bridge: Used to match each intermediary-object to a final-object
getObjects() - Method in class ObjectCollectionProviderUnary
getObjects() - Method in class FeatureInputObjectCollection
getObjects() - Method in class OutputFeatureTable: The objects for which features are calculated.
getObjects() - Method in class ReportFeatureOnObjectsBase
getObjects() - Method in class DistanceTransformForEachObject3D
getObjects() - Method in class LevelPerObjectBase: The objects for whom a level is calculated
getObjects() - Method in class UnaryWithObjectsBase
getObjects() - Method in class GenerateToMatchObjects
getObjects() - Method in class FromObjects
getObjects() - Method in class IntersectsWith
getObjects() - Method in class Always
getObjects() - Method in class Intersection
getObjects() - Method in class Permute
getObjects() - Method in class ColoredObjects: Objects to draw on a background
getObjects() - Method in class ObjectAggregationBase
getObjects() - Method in class ColoredObjectCollection: The objects in the collection.
getObjects() - Method in class FromObjects
getObjects() - Method in class ObjectAsPoints
getObjects() - Method in class IncludeRandomObjects
getObjects() - Method in class PointsFromObjects
getObjects() - Method in class FromObjects
getObjects() - Method in class ExportObjectsBase
getObjects() - Method in class PointsFitterToMark
getObjects1() - Method in class MergeTwoCollectionsItemwise: First collection with items to be merged
getObjects2() - Method in class MergeTwoCollectionsItemwise: Second collection with items to be merged
getObjectsBlue() - Method in class ThreeColoredObjects
getObjectsContainer() - Method in class WithContainerBase
getObjectsElse() - Method in class ReferenceOrElse
getObjectsGreater() - Method in class GreaterIntersectionWith
getObjectsGreen() - Method in class ThreeColoredObjects
getObjectsGrouped() - Method in class FilterByGroup
getObjectsLesser() - Method in class GreaterIntersectionWith
getObjectsRed() - Method in class ThreeColoredObjects
getObjectsRejected() - Method in class ObjectCollectionProviderFilterBase
getObjectsSeeds() - Method in class SegmentChannel
getObjectsSeeds() - Method in class SegmentWithSeeds
getObjectsSource() - Method in class AssignFromIntersectingObjects
getObjectsSource() - Method in class SegmentWithSeeds
getObjectsSplitBy() - Method in class SplitByObjects
getObjectsTarget() - Method in class AssignFromIntersectingObjects
getOffByte() - Method in class Mask
getOffByte() - Method in class BinaryValuesByte: The byte representation of the value for OFF
getOffInt() - Method in class Mask
getOffInt() - Method in class BinaryValues: The integer representation of the value for OFF
getOnByte() - Method in class Mask
getOnByte() - Method in class BinaryValuesByte: The byte representation of the value for ON
getOnInt() - Method in class Mask
getOnInt() - Method in class BinaryValues: The integer representation of the value for ON
GetOperationFailedException - Exception in org.anchoranalysis.core.index: When a get operation fails for a particular key
GetOperationFailedException(Exception) - Constructor for exception GetOperationFailedException
GetOperationFailedException(int, String) - Constructor for exception GetOperationFailedException
GetOperationFailedException(int, Throwable) - Constructor for exception GetOperationFailedException
GetOperationFailedException(String, String) - Constructor for exception GetOperationFailedException
GetOperationFailedException(String, Throwable) - Constructor for exception GetOperationFailedException
getOptimization() - Method in class SegmentWithMarkedPointProcess: The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
getOptional(String) - Method in interface NamedProvider: Retrieves the item if it exists, or returns empty() if it doesn't exist.
getOptional(String) - Method in class NamedProviderBridge
getOptional(String) - Method in class NamedProviderCombine
getOptional(String) - Method in class NameValueSet
getOptional(String) - Method in class EagerEvaluationStore
getOptional(String) - Method in class LazyEvaluationStore
getOptional(String) - Method in class SharedFeatureMulti
getOptional(String) - Method in class NamedStacks
getOptional(String) - Method in class WrapStackAsTimeSequence
getOptional(String) - Method in class WrapStackAsTimeSequenceStore
getOptional(String) - Method in class WrapTimeSequenceAsStack
getOptionList() - Method in class KernelProposer
getOptions() - Method in class BioformatsReader: Options that influence how stack is read.
getOptions() - Method in class ReadOptionsDelegate
getOrCalculate(T) - Method in class ResolvedCalculation: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class ResolvedCalculationMap
getOrCalculate(T) - Method in class FeatureCalculation: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class FeatureCalculationMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCreate(Class<?>) - Method in class SharedObjects: Gets an existing store, or creates a new one
getOrCreateNew(K) - Method in class MapCreate
getOrientation() - Method in class Ellipse
getOrientation() - Method in class Ellipsoid
getOrientationProposer() - Method in class OrientationAndRadiiProposer
getOrientationXYProposer() - Method in class XYOrientationExtendToZ
getOriginal() - Method in class OverlappingObject: Original unscaled element before any operations
getOrNull(U) - Method in class FeatureCalculationMap: Gets an existing result for the current params from the cache.
getOtherwise() - Method in class IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
getOutlineColor() - Method in class SegmentInstanceWithModel: The color of the outline
getOutlinePixelsRetriever() - Method in class TraversePointsOnContour
getOutlinePixelsRetrieverReverse() - Method in class TraversePointsOnContour
getOutlineWidth() - Method in class BoundingBoxOutline
getOutlineWidth() - Method in class Outline
getOutlineWidth() - Method in class CompareAnnotations
getOutlineWidth() - Method in class AtScale
getOutlineWidth() - Method in class ColoredBase: The width of the outline (only relevant if outline==true
getOutlineWidth() - Method in class OutlinePreserveRelativeSize: The width of the outline.
getOutlineWidth() - Method in class SegmentInstanceWithModel: The width of the outline
getOutlineWidth() - Method in class VisualizeOnBackground
getOutlineWidth() - Method in class ExportObjectsAsCroppedImages
getOutPath() - Method in class InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
getOutput() - Method in class OutputExperiment: The output-manager that specifies how/where/which elements occur duing outputting.
getOutput() - Method in class ExperimentExecutor
getOutput() - Method in class QuickMultiDatasetExperiment
getOutputDirectory() - Method in class Outputter
getOutputDirectory() - Method in class OutputterChecked
getOutputDirectory() - Method in class OutputPrefixerSettings: A directory indicating where inputs can be located
getOutputEnabledDelta() - Method in class OutputArguments: Additions/subtractions of outputs for the experiment supplied by the user.
getOutputName() - Method in class ToTextFileBase: The name to use (without extension) for the text-file log
getOutputName() - Method in class FeatureCSVMetadata: The output name for the features CSV.
getOutputName() - Method in class OutputtedFile
getOutputName() - Method in class OutputNameStyle: An identifier used in rules to determine if an output is enabled or not.
getOutputName() - Method in class PeriodicSubdirectoryReporter
getOutputName() - Method in class MinimalExecutionTimeStatsReporter
getOutputName() - Method in class VoxelizedMarksChangeReporter
getOutputNameStyle() - Method in class OutputPattern
getOutputNameStyle() - Method in class FromOutputName
getOutputPattern() - Method in class BoundOutputter
getOutputRGBOutline() - Method in class ExportObjectsAsCroppedImages
getOutputRGBOutlineFlattened() - Method in class ExportObjectsAsCroppedImages
getOutputsDisabled() - Method in class SpecificDisabled: The names of the outputs that are disbled.
getOutputsEnabled() - Method in class SpecificEnabled: The names of the outputs that are enabled.
getOutputsEnabled() - Method in class OutputManager: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class OutputterChecked: Which outputs are enabled or not enabled.
getOutputsEnabled() - Method in class ElementOutputter: Which outputs are enabled or not enabled.
getOutputStackProvider() - Method in class ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputter() - Method in class InitializationContext
getOutputter() - Method in class InputBound
getOutputter() - Method in class InputOutputContextStateful
getOutputter() - Method in class ParametersExperiment
getOutputter() - Method in class BoundOutputter: The outputter to be used for the sequence.
getOutputter() - Method in interface InputOutputContext: An outputter that writes to the particular output-directory.
getOutputter() - Method in class ElementOutputter: The outputter for writing the element.
getOutputter() - Method in class OptimizationContext
getOutputterFor(String) - Method in class SharedStateFilteredImageOutput: groupIdentifierFor should always called at least once before getOutputManagerFor
getOutputWriteSettings() - Method in class OutputManager: General settings (default file extensions, colors etc.) for outtping files.
getOutputWriteSettings() - Method in class QuickExperiment
getOutside() - Method in class UnitsWithinRange: Returned as a constant if a value lies otside the range
getOutsideKernelPolicy() - Method in class KernelApplicationParameters: How to handle voxels that appear in a neighbourhood that lies outside the scene boundaries.
getOverlapRatioThreshold() - Method in class KernelBirthAndKill
getOverlapThreshold() - Method in class ConditionallyMergeOverlappingObjects: The maximum size for merging.
getOverlays() - Method in class ColoredOverlayCollection
getOverlays() - Method in class IndexableOverlays
getPadding() - Method in class TextStyle: Padding added around the text in both dimensions if a default size is inferred (ignored if an explicit size is specified )
getPadding() - Method in class DrawCroppedObjectsGenerator
getPadding() - Method in class ExportObjectsBase: Padding placed on each side of the outputted image (if it's within the image)
getPaddingXY() - Method in class Padding: Padding placed on each side of the outputted image (if it's within the image) in XY directions
getPaddingZ() - Method in class Padding: Padding placed on each side of the outputted image (if it's within the image) in Z direction
getPair() - Method in class MergedPairsFeatures
getPair() - Method in class EnergyPair
getPair() - Method in class MarksWithEnergyBreakdown: Every combination of interactions between marks and the associated energy
getPairAddCriteria() - Method in class EnergySchemeCreatorByElement
getPairAddCriteria() - Method in class EnergyScheme
getPairCollection() - Method in class KernelMerge
getPairsFor(Mark) - Method in class RandomCollectionWithAddCriteria
getPairTypeClass() - Method in class RandomCollectionWithAddCriteria
getParametersExperiment() - Method in class ParametersUnbound
getParamPrefix() - Method in class PermuteFeatureSequenceInteger
getParams() - Method in class HOGDescriptor: Parameters used for calculating HOG
getParams() - Method in class HOGFeature: Parameters used for calculating HOG
getParamsOptional() - Method in class FeatureInputEnergy
getParamsOptional() - Method in interface FeatureInputParams
getParamsOptional() - Method in class FeatureInputMark
getParamsRequired() - Method in interface FeatureInputParams
getParent() - Method in class ErrorNodeImpl
getParentDirectory() - Method in class MutableDirectory
getParentDirectory() - Method in class OutputtedFile
getParentDirectoryCreator() - Method in class OutputterTarget
getParentOutputter() - Method in class PeriodicSubdirectoryReporter
getPartition() - Method in class MarksFromPartition
getPath() - Method in class AnnotationWithStrategy: Path to annotation
getPath() - Method in class NotFound: the path an object was not found at.
getPath() - Method in class RootPath: A path on a filesystem to the directory, that defines the root
getPath() - Method in class SingleFile
getPath() - Method in class NamedFile: The path of NamedFile.getFile().
getPath() - Method in class NamedPath: The path
getPath() - Method in class RootedFilePath
getPath() - Method in class StaticFilePath
getPath() - Method in class FileDetails
getPathAnnotation() - Method in class SinglePathStrategy
getPathDefaultMarks() - Method in class MarkProposerStrategy
getPathLabel() - Method in class ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes)
getPathParams() - Method in class MarkProposerStrategy
getPathParser() - Method in class GroupFiles
getPaths() - Method in class InputArguments: A list of paths referring to specific inputs;
getPaths() - Method in class FileSetFromStringSet
getPaths() - Method in class FilterForExistingFiles: All files need to be present
getPayload() - Method in class TypedEdge: The edge.
getPayload() - Method in class ObjectVertex
getPenaltyValue() - Method in class MaxOverlapRatio
getPeriodTriggerBank() - Method in class FeedbackBeginParameters
getPermutation() - Method in class PermuteFeature: A permutation to apply.
getPermutations() - Method in class PermuteFeature: A list of permutations to apply.
getPermuteProperty() - Method in class Permute
getPermuteProperty() - Method in class PermuteFeatureSequenceInteger
getPixelsForPlane(int) - Method in class EncodedVoxels
getPlotBackgroundColor() - Method in class PlotColorScheme
getPlotGridlineColor() - Method in class PlotColorScheme
getPlusOne() - Method in class SlidingBuffer: The voxel-buffer for the slice with the currently selected slice's index +1 or null if it's the final slice.
getPoint() - Method in class KernelPointCursor: The point around which the cursor may iterate.
getPointFitters() - Method in class PointsInitialization
getPoints() - Method in class PointListBase
getPoints() - Method in class Contour
getPointsFitter() - Method in class CreateMarkFromPoints
getPointsFitter() - Method in class MarkProposerStrategy: Name of the PointsFitter to use.
getPointsFitter() - Method in class FitPoints
getPointsFitter() - Method in class FitPointsFromObjects
getPointsFitter() - Method in class PointsFitterToMark
getPointsFitter() - Method in class ReflectInAxesWithinDistance
getPointsFromOrientationProposer() - Method in class MergeLists
getPointsFromOrientationXYProposer() - Method in class XYOrientationExtendToZ
getPointsProposer() - Method in class FitPoints
getPosition() - Method in class MarkWithPosition
getPositionProposer() - Method in class Position
getPositionProposer() - Method in class Repeat
getPostcondition() - Method in class DilationContext: If defined, a condition which must be satisfied after an iteration occurs, otherwise no more iterations occur.
getPower() - Method in class MeanRaisedToPower
getPredicates() - Method in class PathMatchConstraints: Predicates for both a file and a directory.
getPrefix() - Method in class DefineAdderWithPrefixBean: A prefix that is placed before the name of every bean created
getPrefix() - Method in class PermutePropertySequenceIntegerWithinString
getPrefix() - Method in class PathPrefixerAvoidResolve: A string prefixed to each output-path.
getPrefix() - Method in class OutputterTarget
getPrefix() - Method in class Outputter
getPrefix() - Method in class OutputterChecked
getPrefix() - Method in class ExperimentStructure
getPrefixer() - Method in class OutputArguments: Where outputs are written, and how identifiers are styled.
getPrefixer() - Method in class ParametersExperiment: The OutputManager associated with the experiment which Outputter uses.
getPrefixer() - Method in class OutputManager: Determines a prefix to use when outputting a file based upon an input-path.
getPrefixer() - Method in class PathPrefixerContext: Settings for where and how outputs should be prefixed.
getPrefixer() - Method in class LastDirectoryAsPrefix
getPrefixer() - Method in class Rooted
getPrefixerElse() - Method in class IfIncrementingNumberRequested: Called if the requested condition is not true.
getPrefixerIf() - Method in class IfIncrementingNumberRequested: Called if the requested condition is true.
getPrefixToRemove() - Method in class DirectoryStructure
getPrependColor() - Method in class Prepend
getPrependString() - Method in class ListSequence
getPrependString() - Method in class PrependName
getPrependString() - Method in class DeriveFromPair
getPrependString() - Method in class FeatureListProviderAggregatePair
getPriority() - Method in class PrioritisedVertex
getProbNeg() - Method in class KernelPosNeg
getProbPos() - Method in class KernelPosNeg
getProgress() - Method in class InputManagerParams
getProperties() - Method in class ObjectWithProperties
getProperty(String) - Method in class ObjectWithProperties
getPropertyDefiner() - Method in class InitializableBean
getPropertyInitializer() - Method in class InitializableBean
getPropertyPath() - Method in class PermutePropertyWithPath: Either a direct property of a bean e.g.
getProposal() - Method in class OptimizationStep
getProposal() - Method in class Reporting
getProposalSecondary() - Method in class Reporting: An optional additional marks-Energy that provides an additional explanation of proposed
getProposer() - Method in class MarkFromCollectionProposerUnary
getProposer() - Method in class MarkProposerUnary
getProvider() - Method in class FromProvider
getPxlPartMemo() - Method in class FeatureInputAllMemo
getPxlPartMemo() - Method in class FeatureInputSingleMemo
getQuantile() - Method in class Quantile: The quantile.
getQuantile() - Method in class QuantileStretch
getQuantile() - Method in class Quantile
getQuantile() - Method in class DiscardOutliers
getQuantile() - Method in class Quantile
getQuantile() - Method in class QuantileAcrossObjects
getQuantile() - Method in class QuantileAcrossConnectedComponents
getQuantileHigh() - Method in class Range
getQuantileLow() - Method in class Range
getQuantileLower() - Method in class ToByteUpperLowerQuantileIntensity
getQuantileUpper() - Method in class ToByteUpperLowerQuantileIntensity
getRadii() - Method in class Ellipse
getRadii() - Method in class Ellipsoid
getRadiiProposer() - Method in class OrientationAndRadiiProposer
getRadiiProposer() - Method in class RadiiProposerRepeat
getRadius() - Method in class MarkWithPositionAndSingleRadius
getRadius() - Method in class AutoLocalThreshold
getRadius() - Method in class WithRadiusBase
getRadiusBound() - Method in class UniformRandomRadiiProposer
getRadiusX() - Method in class FitResult
getRadiusY() - Method in class FitResult
getRadiusZ() - Method in class FitResult
getRandomNumberGenerator() - Method in class ProposerContext
getRangeAxisLimits() - Method in class PlotInstance
getRangeC() - Method in class SizeExtents
getRangeT() - Method in class SizeExtents
getRangeZ() - Method in class SizeExtents
getRate() - Method in class Geometry
getRaw() - Method in class UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at the current buffer position.
getRaw(int) - Method in class UnsignedByteBuffer: Gets an unsigned-byte (represented as a byte) at a particular buffer position.
getRaw() - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as an int) at the current buffer position.
getRaw(int) - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a int) at a particular buffer position.
getRaw() - Method in class UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at the current buffer position.
getRaw(int) - Method in class UnsignedShortBuffer: Gets an unsigned-short (represented as a short) at a particular buffer position.
getReaderMatching() - Method in class BranchExtension: The reader to use if the extension matches.
getReaderNotMatching() - Method in class BranchExtension: The reader to use if the extension does not match.
getReason() - Method in class NotFound
getReceive() - Method in class CombineBase
getRecordedOutputs() - Method in class RecordedOutputsWithRules: If defined, records output-names that are written / not-written during the experiment.
getRed() - Method in class RGBColorBean
getRed() - Method in class RGBColor
getRed() - Method in class ThreeChannels
getReduce() - Method in class FeatureListProviderAggregatePair: Method for reducing all pairs into a single value e.g.
getReduce() - Method in class SuppressNonMaxima: The algorithm for reducing the number of object-masks.
getReferencePoissonIntensity() - Method in class MarkWithIdentifierFactory
getReferencesFeatureListCreator() - Method in class ReferencedFeatures: Ensures any feature-lists mentioned here are evaluated, before this list is created.
getReferencesFeatureListCreator() - Method in class PermuteFeature: Makes sure a particular feature list creator is evaluated
getRegex() - Method in class RegularExpressionBase
getRegEx() - Method in class RegExMatcher
getRegEx() - Method in class PathRegEx: Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class RemoveMatching: If a path matches a regular expression it is removed.
getRegEx() - Method in class Exclude
getRegEx() - Method in class InsertRegExGroups: The regular-expression to use for matching groups.
getRegEx() - Method in class JoinRegExGroups
getRegex() - Method in class Replace: Regular expression to match against string
getRegex() - Method in class QuickBase: A regular-expression applied to the image file-path that matches three groups.
getRegEx() - Method in class ExperimentStructure
getRegexAdjacent() - Method in class NamedChannelsQuick: This needs to be set if there is at least one adjacentChannel.
getRegExDir() - Method in class MultiFileReader: If non-empty a regular-expression is applied to directories
getRegExFile() - Method in class MultiFileReader: If non-empty a regular-expression is applied to files
getRegion() - Method in class Thresholded
getRegion() - Method in class Intensity
getRegionID() - Method in class RegionMembershipWithFlags
getRegionID() - Method in class VolumeMin
getRegionID() - Method in class FromMarks
getRegionID() - Method in class IndexedRegionBase
getRegionID() - Method in class ColoredMarks
getRegionID() - Method in class FeatureMarkRegion
getRegionID() - Method in class FeatureSingleMemoRegion
getRegionID() - Method in class FeaturePairMemoSingleRegion
getRegionID() - Method in class KernelBirthAndKill
getRegionMap() - Method in class EnergySchemeCreatorByElement
getRegionMap() - Method in class EnergyScheme
getRegionMap() - Method in class EnergySchemeWithSharedFeatures
getRegionMap() - Method in class EnergyMemoList
getRegionMap() - Method in class VoxelizedMarkMemo
getRegionMap() - Method in class ProposerContext
getRegionMap() - Method in class FromMarks
getRegionMap() - Method in class AsObject
getRegionMap() - Method in class SurfaceSizeMaskNonZero
getRegionMembership() - Method in class RegionMembershipWithFlags
getRejectionReason() - Method in class DualMarksAnnotation
getRelation() - Method in class RelationToConstant
getRelation() - Method in class ObjectFilterRelation
getRelation() - Method in class MergePairs: Relation to threshold
getRelation() - Method in class IdentityImposeValueRelationToHistogram
getRelation() - Method in class RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
getRelation() - Method in class AddCriteriaFeatureRelationThreshold
getRelation() - Method in class RequireFeatureRelationThreshold
getRemainder() - Method in class SplitPath
getRepeat() - Method in class MovieFromSlices
getRepeats() - Method in class KernelBirth: Total number of births
getRepeatZProvider() - Method in class GenerateString: Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
getReplacement() - Method in class SubstituteRegularExpression
getReplacement() - Method in class Replace: What to replace in the path
getReplacement() - Method in class AdjacentFile: The replacement string used to determine the file
getRequireArguments() - Method in class OnlyIf: The conditions that must be fulfilled
getRequireArguments() - Method in class FeedbackReceiverRequireArguments
getResizeTo() - Method in class GroupedMeanChannelTask: If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
getResizeTo() - Method in class HOGDescriptor: The input-image is rescaled to this width/height before calculating HOG descriptors
getResizeTo() - Method in class HOGFeature: The input is rescaled to this width/height before calculating HOG descriptors
getResolution() - Method in class BinarySegmentationParameters
getResolutionOptional() - Method in class FeatureInputEnergy
getResolutionOptional() - Method in interface FeatureInputWithResolution
getResolutionOptional() - Method in class FeatureInputHistogram
getResolutionOptional() - Method in class FeatureInputMarkCollection
getResolutionOptional() - Method in class FeatureInputMark
getResolutionRequired() - Method in interface FeatureInputWithResolution
getRestrictTo() - Method in class Invert: If set, the inversion only occurs on a particular region of the mask, as determined by this mask
getResults() - Method in class FeatureInputResults
getResultsVector() - Method in class ResultsVectorWithThumbnail
getRGB() - Method in class RGBColorBean
getRGB() - Method in class RGBColor
getRight() - Method in class ObjectsToCompare: Objects on right-side of the comparison
getRoot() - Method in class SplitPath
getRoot() - Method in class ProposerFailureDescription
getRoot() - Method in class TestLoader
getRoot1() - Method in class QuadraticEquationSolver.QuadraticRoots
getRoot2() - Method in class QuadraticEquationSolver.QuadraticRoots
getRootDirectory() - Method in class Manifest
getRootName() - Method in class Rooted: The name of the root-path to associate with this fileset.
getRootName() - Method in class RootedFilePath
getRootName() - Method in class Rooted
getRootName() - Method in class Rooted
getRootName() - Method in class QuickBase: If non-empty then a rooted filesystem is used with this root
getRootName() - Method in class RootedExperiment: Root-name assuming multi-rooted structure.
getRootNameForStructure() - Method in class ExperimentResultsExperimentStructure: If rootInStructure==true, the rootName is placed in the folder structure.
getRootPath() - Method in class DeserializedManifest
getRotationAngle() - Method in class BoundRotation2D
getRotationMatrix() - Method in class OrientationRotationMatrix
getRotationX() - Method in class BoundRotation3D
getRotationY() - Method in class BoundRotation3D
getRotationZ() - Method in class BoundRotation3D
getRotMatrix() - Method in class FitResult
getRow(int) - Method in class TableItemArrangement
getRow() - Method in class Cell
getRowForListIndex(int) - Method in class TableItemArrangement
getRowSource() - Method in class InputProcessContext
getSampleEvery() - Method in class SampleWithDirectory
getScalarProposer() - Method in class MaxWithConstant
getScalarProposer() - Method in class Scale
getScale() - Method in class FirstSecondOrderStatistic: Standard-Deviation
getScale() - Method in class MontageSlices: Whether to increase or reduce the size of the images
getScaleCalculator() - Method in class ScaleXY
getScaleCalculator() - Method in class ScaleXY: Determines how much to scale by
getScaleCalculator() - Method in class Scale
getScaleCalculator() - Method in class AtScale
getScaleCalculator() - Method in class Invert: The delegate ScaleCalculator whose calculation will be inverted.
getScaleCalculator() - Method in class ScaleImage: Calculates what scale-factor to apply on the image.
getScaleCalculator() - Method in class ScaleXY
getScaleFactor() - Method in class GradientBase
getScaleInput() - Method in class SegmentObjectsFromTensorFlowModel: Any scaling to be applied to the input-image before being input to the model for inference.
getScaleLower() - Method in class ToByteUpperLowerQuantileIntensity: Sets the min by multiplying the quantileLower by this constant.
getScaleLower() - Method in class ScaleByParams
getScaleRadii() - Method in class ConicFitterBase
getScaleUpper() - Method in class ToByteUpperLowerQuantileIntensity: Sets the max by multiplying the quantileUpper by this constant.
getScaleUpper() - Method in class ScaleByParams
getScore() - Method in class ScoreVoxels
getScoreExtracter() - Method in class AcceptanceProbabilityCalculator
getScoreProvider() - Method in class ExtractSlice
getScoreThreshold() - Method in class RemoveOverlappingObjects: Bounding boxes with scores above this threshold are removed
getSearchObjects() - Method in class FeatureIntersectingObjects
getSecond() - Method in class CostMatrix
getSecond() - Method in class FeatureInputPairObjects
getSecond() - Method in class OutputEnableRulesSpecify: Output-names in the second-level (for all first level output-names)
getSecond() - Method in class Compose: Second transformation from U to T
getSecondary() - Method in class StateReporterToPixelized
getSegment() - Method in class BinarySegmentationOne
getSegment() - Method in class SegmentChannelIntoObjectsUnary
getSegment() - Method in class SegmentChannel: Segmentation algorithm
getSegment() - Method in class SegmentChannel
getSegment() - Method in class SegmentChannelByObject
getSegment() - Method in class SegmentStack: The segmentation procedure.
getSegment() - Method in class SegmentWithSeeds
getSegment() - Method in class ConnectedComponentsFromBinarySegmentation
getSegment() - Method in class SegmentInstanceWithModel: The segmentation algorithm
getSegment() - Method in class SegmentMarksFromImage: How to perform the segmentation.
getSegment() - Method in class SuppressNonMaxima: The segmentation algorithm that is applied as an input to non-maxima suppression.
getSegmentStack() - Method in class SegmentOnMaximumIntensityAndExpandInZ
getSelect() - Method in class DeriveFromPair: Either "merged" or "first" or "second" indicating which feature to delegate from
getSelectChannels() - Method in class GroupedStackBase: Selects which channels are included, optionally renaming.
getSemiMajorAxis() - Method in class EllipseStandardFormConverter
getSemiMinorAxis() - Method in class EllipseStandardFormConverter
getSeperator() - Method in class ListSequence
getSeperator() - Method in class CombineCSV
getSequence() - Method in class PermutePropertySequence: Where the sequence starts
getSequence() - Method in class ListSequence: First number range that is appended
getSequence() - Method in class ChangeableOutputSequence
getSequenceAdditional() - Method in class ListSequence: Another number range that is appended
getSequenceType() - Method in class OutputSequenceIndexed
getSequenceType() - Method in class ManifestDirectoryDescription: A sequence-type to describe the different filenames outputted in the directory.
getSeriesColors() - Method in class PlotIndexBaseCategorical
getSeriesNameFor(int) - Method in class PlotIndexBase
getSet() - Method in class SharedFeatureSet
getSettings() - Method in class Outputter
getSettings() - Method in class OutputterChecked: General settings for outputting.
getSettings() - Method in class OutputWriteContext: User-define settings for outputting in output-manager.
getSettings() - Method in class ElementOutputter: General settings for outputting.
getSharedFeatures() - Method in class FeaturesInitialization
getSharedFeatures() - Method in class EnergySchemeSet
getSharedFeatures() - Method in class EnergySchemeWithSharedFeatures
getSharedObjects() - Method in class FeatureInitialization
getSharedObjects() - Method in class ImageInitialization
getSharedState() - Method in class InputBound
getSharedState() - Method in class ParametersUnbound
getSharedState() - Method in class CopyContext: State shared across all inputs when copying.
getSharedState() - Method in class SharedStateRememberConverted: The shared state.
getShellRad() - Method in class MarkEllipseFactory
getShellRad() - Method in class MarkEllipsoidFactory
getShellRad() - Method in class Ellipse
getShellRad() - Method in class Ellipsoid
getShellRad() - Method in class FromObjects
getShellRad() - Method in class CreateEllipse
getShellRad() - Method in class ConicFitterBase
getShortTitle() - Method in class Plot: A shortened version of Plot.getTitle().
getShowOngoingJobsLessThan() - Method in class ParallelProcessor: When the number of ongoing jobs is less than this threshold, they are shown in event logs.
getSigma() - Method in class BlurStrategy
getSigma() - Method in class GaussianBlur2D
getSimplePairCollectionID() - Method in class KernelMerge
getSingle() - Method in class MergedPairsFeatures
getSize() - Method in class TaskArguments: Suggests dimensions or a scaling-factor to resize an image to.
getSize() - Method in class TextStyle: Explicit size of the image the string is draw on
getSize() - Method in class Kernel
getSize() - Method in class Aggregator
getSize() - Method in class PlotHistogram: Size of the image produced showing a plot of the histogram
getSize() - Method in class OutlinePreserveRelativeSize: Size of all created thumbnails
getSize() - Method in class ScaleToSize
getSize() - Method in class MovieFromSlices
getSize() - Method in class IntegerRange
getSizeHalf() - Method in class Kernel
getSizeXY() - Method in class SpecifyDimensions: Length of X and Y dimensions.
getSizeZ() - Method in class SpecifyDimensions: Length of Z dimension.
getSkipFirstTrim() - Method in class RemoveTrailingDirectory
getSkipFirstTrim() - Method in class FilePathAppendBase
getSkipNumberSubdirectories() - Method in class LastDirectories: Initially skip this number of directories before including them in the description.
getSlice(int) - Method in interface VoxelPartition
getSlice(int) - Method in class VoxelPartitionHistogram
getSlice() - Method in class RepeatSlice
getSliceFirst() - Method in class MontageSlices: First slice.
getSliceID() - Method in class SelectSlicesBase: Index of slice to use, or -1 to use all slices
getSliceIndex() - Method in class RepeatSlice: Which slice to use from mask
getSliceIndex() - Method in class FileDetails
getSliceLast() - Method in class MontageSlices: Last slice.
getSmoothingFactor() - Method in class SplitContourAtSaddlePoints
getSource() - Method in class StringMapItem
getSource() - Method in class MatchedObject: The source object (which is matched against others)
getSource() - Method in class IdentifiablePair
getSource() - Method in class PairPxlMarkMemo
getSource() - Method in class ExportFeatures: Source of feature-values to be exported
getSource() - Method in class DualVoxelizedMarks
getSource() - Method in class ToPixelized
getSourceDirectory() - Method in class CopyContext: Source directory of copying.
getSplitDescriptiveNameRegex() - Method in class CompareAnnotations
getSplitProposer() - Method in class KernelSplit
getSquareSize() - Method in class SplitIntoSquares
getStack() - Method in class StackProviderUnary
getStack() - Method in class DisplayStack
getStack() - Method in class StackProviderWithLabel
getStack() - Method in class ColoredMarksWithDisplayStack
getStack() - Method in class MarksWithDisplayStack
getStack() - Method in class FromStack: Provides a stack.
getStack() - Method in class SegmentStack: The stack to segment
getStack() - Method in class ExportObjectsFromCSV: The stack that is the background for our objects
getStackEnergy() - Method in class FeatureEvaluator: Optionally specifies an energy-stack to be associated with every calculation input.
getStackEnergy() - Method in class FromImage: Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
getStackEnergy() - Method in class BinaryClassifierImageLabeller
getStackEnergy() - Method in class ExtractSlice
getStackEnergy() - Method in class DefineOutputterWithEnergy
getStackID() - Method in class IfStackExists
getStackName() - Method in class One: If defined, processing only occurs the stack with this specific stack and index.
getStackNameVisualOriginal() - Method in class AnnotationBackground
getStackProviderID() - Method in class FromStack: Specifies the ID of an existing stack.
getStackProviderID() - Method in class FromStackChannel
getStackReader() - Method in class AnnotatorStrategy
getStackReader() - Method in class InputManagerWithStackReader
getStackReader() - Method in class MaskComparer
getStackReader() - Method in class AnnotationComparisonInput
getStackReader() - Method in class FlattenAsChannel: Reads the image that is subsequently flattened.
getStackReader() - Method in class ImposeResolution: Reads an image before a resolution is imposed.
getStackReader() - Method in class MultiFileReader
getStackReader() - Method in class ReadVoxelExtentXml: Reads an image before a resolution is imposed.
getStackReader() - Method in class RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
getStackReaderAdjacent() - Method in class NamedChannelsQuick: The raster-reader to use for opening any adjacent-channels
getStackReaderAppend() - Method in class QuickBase: The raster-reader for reading any appended files
getStackStore() - Method in class ChannelSource
getStart() - Method in class SequenceInteger: The index to begin iteration from
getStartIndex() - Method in class IndexRange: The index if the first element to use in the subsetting range, zero-indexed.
getStartIndex() - Method in class MovieFromSlices
getStartingIntensity() - Method in class FloodFillEachIntensityLevel: The first intensity-value to consider as a valid object (e.g.
getStartPoint() - Method in class LineSegment
getState() - Method in class FeedbackEndParameters
getStateReporter() - Method in class TransformationAssignMode
getStrategy() - Method in class AnnotationWithStrategy
getStrategy() - Method in class BoundReplaceStrategy
getStrategy() - Method in class Blur
getStringRasterGenerator() - Method in class GenerateString
getSubdirectory() - Method in class AppendDictionary
getSubdirectory() - Method in class ExperimentResultsExperimentStructure: If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
getSubdirectoryName() - Method in class OutputPattern: The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
getSubtractConstant() - Method in class IntensityGradientBase
getSubtractRadii() - Method in class ConicFitterBase
getSuffix() - Method in class PermutePropertySequenceIntegerWithinString
getSuggestedFormatToWrite() - Method in class StackWriteOptions: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class OutputWriteContext: A suggestion on what file-format to write.
getSuggestedFormatToWrite() - Method in class ElementOutputter
getSuggestedImageOutputFormat() - Method in class OutputPrefixerSettings: A file format suggested for writing images to the file system.
getSuggestedResize() - Method in class InitializationContext: A suggested input on how to resize an image, if one is provided.
getSuggestedResize() - Method in class ImageInitialization
getSum() - Method in class RunningSum: The running sum
getSummarizer() - Method in class SummarizerInputFromManager
getSummarizer() - Method in class SummarizeBase
getSummarizerElse() - Method in class SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
getTarget() - Method in class StringMapItem
getTask() - Method in class JobProcessor
getTask() - Method in class ExperimentExecutor
getTask() - Method in class ConvertNamedChannels: The underlying task that will be called, perhaps with a different input-type.
getTask() - Method in class QuickExperiment
getTask() - Method in class QuickMultiDatasetExperiment
getTask() - Method in class QuickMultiDatasetStructuredExperiment
getTaskArguments() - Method in class InputBound
getTaskName() - Method in class TaskArguments: A name to describe the ongoing task.
getTaskProcessor() - Method in class InputOutputExperiment: What task is associated with the experiment, and how it is processed.
getTemperature() - Method in class Aggregator
getTemperature() - Method in class Reporting
getTemplateMark() - Method in class MarkWithIdentifierFactory
getTemporary() - Method in class EncodedVoxels
GetterFromIndex<T> - Interface in org.anchoranalysis.core.index
getTermination() - Method in class SimulatedAnnealing
getText() - Method in class GenerateString: Text to draw on an image
getThreshold() - Method in class RelationToConstant
getThreshold() - Method in class CutBelowThreshold
getThreshold() - Method in class CalculateLevelRelativeToThreshold
getThreshold() - Method in class IntensityGreaterEqualThan
getThreshold() - Method in class ThresholdedFeature
getThreshold() - Method in class ThresholdedVolume
getThreshold() - Method in class Count
getThreshold() - Method in class RatioThreshold
getThreshold() - Method in class FeatureIntersectingObjectsThreshold: Only considers values greater or equal to the threshold
getThreshold() - Method in class AddCriteriaFeatureRelationThreshold
getThreshold() - Method in class RequireFeatureRelationThreshold
getThreshold() - Method in class GreatestAreaSlice
getThreshold() - Method in class Thresholded
getThreshold() - Method in class IfCondition
getThresholder() - Method in class BinarySegmentationThreshold
getThresholder() - Method in class Threshold: The thresholder that will convert a channel into a binary-channel
getThumbnail() - Method in class CombineObjectsForFeatures: Generates a thumbnail representation of one or more objects combine, as form a single input
getThumbnail() - Method in class FromImage: Method to generate a thumbnail for images
getThumbnail() - Method in class ResultsVectorWithThumbnail
getThumbnailBatch() - Method in class ListWithThumbnails
getTime() - Method in class JobState
getTimeAnnotationLastUpdated() - Method in class DualMarksAnnotation: Number of seconds since the UNIX epoch
getTimeIndex() - Method in class ConvertNamedChannelsToStack
getTimeIndex() - Method in class FileDetails
getTimeIndexGroupID() - Method in class RegularExpression
getTimes() - Method in class Repeat
getTitle() - Method in class ReportFeatureEvaluator
getTitle() - Method in class Plot: The full title of the plot.
getTitle() - Method in class ReportFeatureForManifestFileBase
getTo() - Method in class TypedEdge: The vertex the edge joins to.
getTolerance() - Method in class UnchangedScore: An exponent of 10 which determines a tolerance, less than which a score will be deemed unchanged compared to another.
getTotal() - Method in class EnergyTotal
getTotalCount() - Method in class Histogram
getTotalNumberTasks() - Method in class ConcurrentJobMonitor
getTransformer() - Method in class RemovePartitionAndThen
getTransformer() - Method in class VoxelizeWithTransform
getTransformer() - Method in class KernelStateBridgePixelize
getTransformerKernelToState() - Method in class KernelStateBridgeTransformer
getTransformerMarks() - Method in class AddDualTransformer
getTransformerPrimary() - Method in class StateReporterTransformer
getTransformerSecondary() - Method in class StateReporterTransformer
getTransformerStateToKernel() - Method in class KernelStateBridgeTransformer
getTriggerTerminationCondition() - Method in class OptimizationContext
getTrimTrailingDirectory() - Method in class RemoveTrailingDirectory
getTrimTrailingDirectory() - Method in class FilePathAppendBase
getType() - Method in class ManifestDescription: Identifies the type of entity.
getUnconvertedVoxelAt(int, Point3i) - Method in class DisplayStack
getUniqueLabel() - Method in class AnnotationLabel: Label that uniquely identifies the ID (for machine purposes)
getUnit() - Method in class BoundingBoxExtent
getUnit() - Method in class FeatureSingleMemoRegion
getUnitConverterOptional() - Method in class FeatureInputEnergy
getUnitType() - Method in class DistancePhysical
getUnitType() - Method in class AreaPhysical
getUnitType() - Method in class VolumePhysical
getUnitType() - Method in class FeatureConvertUnits
getUnitType() - Method in class UnitConverter
getUnitTypeFrom() - Method in class ConvertUnits
getUnitTypeTo() - Method in class ConvertUnits
getUnitValueDistance() - Method in class FromUnitValueDistance
getUnsigned() - Method in class UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at the current buffer position.
getUnsigned(int) - Method in class UnsignedBufferAsInt: Gets an unsigned-byte (represented as a int) at a particular buffer position.
getUnsigned() - Method in class UnsignedByteBuffer
getUnsigned(int) - Method in class UnsignedByteBuffer
getUnsigned() - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at the current buffer position.
getUnsigned(int) - Method in class UnsignedIntBuffer: Gets an unsigned-int (represented as a long) at a particular buffer position.
getUnsigned() - Method in class UnsignedShortBuffer
getUnsigned(int) - Method in class UnsignedShortBuffer
getUnsignedByte() - Static method in class VoxelsFactory
getUnsignedInt() - Static method in class VoxelsFactory
getUnsignedShort() - Static method in class VoxelsFactory
getUserFriendlyLabel() - Method in class AnnotationLabel: Descriptive user-friendly label displayed via GUI
getValue() - Method in class NamedBean
getValue() - Method in interface NameValue: The associated value
getValue() - Method in class SimpleNameValue
getValue() - Method in class TypedValue
getValue() - Method in class Constant
getValue() - Method in class DistancePhysical
getValue() - Method in class DistanceVoxels
getValue() - Method in class UnitValueArea
getValue() - Method in class VolumePhysical
getValue() - Method in class VolumeVoxels
getValue() - Method in class OptionalNameValue: The value.
getValue() - Method in class AssignValue
getValue() - Method in class CreateNew
getValue() - Method in class UnaryWithValueBase
getValue() - Method in class EmptyHistogramConstant
getValue() - Method in class IfParamEqual
getValue() - Method in class DictionaryCondition: The value the key should have in the dictionary, in order for the condition to be fulfilled.
getValue() - Method in class ConstantScaleFactor
getValue() - Method in class CountEqual
getValue() - Method in class IdentityImposeValueRelationToHistogram
getValue() - Method in class NormalizeByConstant
getValue() - Method in class Constant
getValue() - Method in class Constant
getValue() - Method in class WithValueBase
getValueIfEmpty() - Method in class FeatureHistogramStatistic: The value to return iff exceptionifEmpty is false
getValueIfTooFewVoxels() - Method in class ImageMomentsBase: A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate moments
getValueNoObject() - Method in class ScoreObjects
getValueNoObjects() - Method in class FeatureIntersectingObjects
getValues() - Method in class PermutePropertyDoubleSet
getValues() - Method in class PermutePropertyStringSet: The values of the string-set
getVersion() - Method in class ExperimentIdentifierConstant
getVertex() - Method in class PrioritisedVertex
getVerticalAlign() - Method in class Overlay
getVisitScheduler() - Method in class TraverseOutlineOnImage
getVoxelDataType() - Method in class Channel
getVoxelDataType() - Method in class VoxelsWrapper
getVoxels() - Method in class SlidingBuffer: The voxels from which buffers corresponding to slices are extracted.
getVoxelsConverter() - Method in class MaxIntensity
getVoxelsConverter() - Method in interface ChannelConverterAttached
getVoxelsConverter() - Method in class MaxIntensityFromHistogram
getVoxelsConverter() - Method in class QuantileIntensityFromHistogram
getVoxelsConverter() - Method in class UpperLowerQuantileIntensityFromHistogram
getVoxelsConverter() - Method in class ChannelConverter
getWeight() - Method in class WeightedKernel
getWeight() - Method in class KernelProposerOptionSingle
getWeightBackground() - Method in class OtsuWeighted
getWeightedKernelFactory(int) - Method in class KernelProposer
getWeightForeground() - Method in class OtsuWeighted
getWeightItem1Greater() - Method in class Range
getWeightItem2Greater() - Method in class Range
getWeightNegative() - Method in class KernelProposerOption
getWeightNegative() - Method in class KernelProposerOptionDual
getWeightNegative() - Method in class KernelProposerOptionSingle
getWeightPositive() - Method in class KernelProposerOption
getWeightPositive() - Method in class KernelProposerOptionDual
getWeightPositive() - Method in class KernelProposerOptionSingle
getWeightWidthDescription() - Method in class WholeImageLabelStrategy
getWhenBinaryChannel() - Method in class BranchChannels: Writer employed if a stack is a single-channeled binary image.
getWhenDetailed() - Method in class SwitchDetailedLogging: Logger to use when detailed-logging is on
getWhenEqual() - Method in class IfParamEqual
getWhenFalse() - Method in class IfElse
getWhenNot() - Method in class SwitchDetailedLogging: Logger to use when detailed-logging is off
getWhenNotEqual() - Method in class IfParamEqual
getWhenRelative() - Method in class IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
getWhenRGB() - Method in class BranchChannels: Writer employed if a stack is a three-channeled RGB image.
getWhenSingleChannel() - Method in class BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
getWhenThreeChannels() - Method in class BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
getWhenTrue() - Method in class IfElse
getWidth() - Method in class SizeXY: Size in X dimension.
getWidth() - Method in class Difference: Width (what the difference is divided by)
getWidth() - Method in class ImposeResolution: Physical pixel size of a voxel in x-dimension.
getWidthFactor() - Method in class DifferenceCalculateLevelStandardDeviation
getWindowSize() - Method in class CenterSliceWindow
getWindowSize() - Method in class HOGParameters: The window-size as per OpenCV implementation.
getWithConfidence() - Method in class LabelledWithConfidence: The element with associated confidence.
getWithin() - Method in class UnitsWithinRange: Returned as a constant if a value lies within the range
getWithinValue() - Method in class CompareWithRange: Constant to return if value lies within the range
getWithinValue() - Method in class CompareWithRangeFeature: Constant to return if value lies within the range
getWriter() - Method in class Flatten
getWriter() - Method in class TextFileOutput
getWriter() - Method in class BranchChannels: Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class WriteResolutionXml
getWriterAlways2D() - Method in class BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class BranchStack: Otherwise the writer to use.
getWriterIfNoSuggestion() - Method in class BranchSuggestedFormat: The writer to use if there is no suggested file-format.
getWriterInstance(Class<?>) - Method in class OutputWriteSettings: Gets a writer-instance for a particular writerParentClass.
getWriters() - Method in class OutputWriteSettings: Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
getWriters() - Method in class OutputterChecked: The writers associated with this output-manager.
getWritersIfSuggested() - Method in class BranchSuggestedFormat: A list of writers to select if a given format is used
getX() - Method in class VectorInDirection
getX() - Method in class PlotAxisLabels
getXDiv() - Method in class Orientation
getXmlAggregatedGroup() - Method in class ResultsWriterOutputNames: The name of the XML file outputted with aggregated values for each group, if enabled.
getXMLConfiguration() - Method in class Experiment
getY() - Method in class VectorInDirection
getY() - Method in class PlotAxisLabels
getYAxisLowerMargin() - Method in class LinePlot
getYAxisUpperMargin() - Method in class LinePlot
getYVal(T, int) - Method in interface LinePlot.YValGetter
getYValGetter() - Method in class BarPlot
getYValGetter() - Method in class LinePlot
getZ() - Method in class VectorInDirection
getZAlign() - Method in class Overlay
getZSliceGroupID() - Method in class RegularExpression
getZSliceNum() - Method in class SortedSetSlice
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
GlobExtractor - Class in org.anchoranalysis.io.input.path: Extracts a glob from a string describing it, and a direcory which gives it context.
GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path
GlobWithDirectory(Optional<String>, String) - Constructor for class GlobExtractor.GlobWithDirectory
GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
GradientBase() - Constructor for class GradientBase
GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
GradientBaseAddSum() - Constructor for class GradientBaseAddSum
gradientCalculation() - Method in class IntensityGradientBase
GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Extracts the gradient in the direction of a particular axis (identified by an index)
GradientForAxis() - Constructor for class GradientForAxis
GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMagnitude() - Constructor for class GradientMagnitude
GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient: Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
GradientMeanForAxis() - Constructor for class GradientMeanForAxis
GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient: Gradient in x and y axes
GradientXY() - Constructor for class GradientXY
GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
GraphLogger(DescribeGraph, Logger) - Constructor for class GraphLogger
GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, where edges contain no payload.
GraphWithoutPayload(boolean) - Constructor for class GraphWithoutPayload: Creates the graph.
GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph: A graph, either directed or undirected, with edges containing a payload of type E.
GraphWithPayload(boolean) - Constructor for class GraphWithPayload: Creates the graph.
GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
GrayscaleReconstruction2DIJ() - Constructor for class GrayscaleReconstruction2DIJ
GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionByErosion() - Constructor for class GrayscaleReconstructionByErosion
GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
GrayscaleReconstructionRobinson() - Constructor for class GrayscaleReconstructionRobinson
greaterEqualThan(VarianceCalculator) - Method in class VarianceCalculator
GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent: Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
GreaterIntersectionWith() - Constructor for class GreaterIntersectionWith
GreaterThan - Class in org.anchoranalysis.math.relation
GreaterThan() - Constructor for class GreaterThan
GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
GreaterThanBean() - Constructor for class GreaterThanBean
GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
GreaterThanEqualTo() - Constructor for class GreaterThanEqualTo
GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
GreaterThanEqualToBean() - Constructor for class GreaterThanEqualToBean
GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider: Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
GreaterThanThreshold() - Constructor for class GreaterThanThreshold
GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
GreatestAreaSlice() - Constructor for class GreatestAreaSlice
greedyMatch() - Method in class HungarianAlgorithm: Find a valid matching by greedily selecting among zero-cost matchings.
GREEN - Static variable in class RGBChannelNames: Name for the green channel.
green() - Method in class RGBStack
GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label: A set of annotation labels partitoned into their unique groups
GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class GroupedAnnotationLabels
groupedLabels() - Method in class WholeImageLabelStrategy
GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster: Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value across the group.
GroupedMeanChannelTask() - Constructor for class GroupedMeanChannelTask
GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Commonality between shared state for gouped export tasks
GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class GroupedSharedState
GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped: Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class GroupedStackBase
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group: An input-manager that can group together files to form stacks or time-series based on finding patterns in the file path (via regular expressions)
GroupFiles() - Constructor for class GroupFiles
groupForKey(String) - Method in class AnnotationComparisonAssigner
groupForKey(String) - Method in class FeatureCostAssigner
groupForKey(String) - Method in class MaskIntersectionAssigner
GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a set of definitions of classes can be collectively grouped using this class.
GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, String, Supplier<T>) - Constructor for class GroupMapByName: Creates a group-map.
groupNameSet() - Method in class IndexedCSVRows
GroupWriter - Class in org.anchoranalysis.feature.io.results.group: Writes outputs pertaining to groups to the filesystem.
GroupWriter(ResultsWriterMetadata) - Constructor for class GroupWriter
growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels: Grows buffer of the object-mask in positive and negative directions by a certain amount.
growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class ObjectMask
growBy(Tuple3i, Extent) - Method in class BoundingBox
growBy(int) - Method in class Extent
growBy(ReadableTuple3i) - Method in class Extent
growToZ(int) - Method in interface Seed
growToZ(int) - Method in class SeedCollection
growToZ(int) - Method in class SeedObjectMask
growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
growToZ(int) - Method in class ObjectMask
guaranteedImageAttributes() - Method in class AssignmentGenerator
guaranteedImageAttributes() - Method in class ChannelGenerator
guaranteedImageAttributes() - Method in class ObjectsAsGrayscaleGenerator
guaranteedImageAttributes() - Method in class ObjectAsMaskGenerator
guaranteedImageAttributes() - Method in class ObjectsAsRGBGenerator
guaranteedImageAttributes() - Method in class DrawObjectOnStackGenerator
guaranteedImageAttributes() - Method in class ExtractBoundingBoxAreaFromStackGenerator
guaranteedImageAttributes() - Method in class DisplayStackGenerator
guaranteedImageAttributes() - Method in class FlattenStackGenerator
guaranteedImageAttributes() - Method in class RasterGenerator: Guarantees on the attributes of all images created by the generator.
guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToDisplayStack
guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToRaster
guaranteedImageAttributes() - Method in class StackGenerator
guaranteedImageAttributes() - Method in class MarksAsUniqueValueGenerator
guaranteedImageAttributes() - Method in class MarksGeneratorBase
GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider: Guesses dimensions from the input-image if it exists.
GuessDimensions() - Constructor for class GuessDimensions

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ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object: Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
ObjectAggregationBase() - Constructor for class ObjectAggregationBase
ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes an object-mask as a mask (i.e.
ObjectAsMaskGenerator() - Constructor for class ObjectAsMaskGenerator: Creates using a default image-resolution.
ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class ObjectAsMaskGenerator
ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
ObjectAsPoints() - Constructor for class ObjectAsPoints
ObjectCollection - Class in org.anchoranalysis.image.voxel.object: A collection of ObjectMask
ObjectCollection() - Constructor for class ObjectCollection: Creates with no objects
ObjectCollection(Stream<ObjectMask>) - Constructor for class ObjectCollection: Creates with elements from a stream
ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object: Creates ObjectCollection using various utility and helper methods
ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
ObjectCollectionProvider() - Constructor for class ObjectCollectionProvider
ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
ObjectCollectionProviderFilterBase() - Constructor for class ObjectCollectionProviderFilterBase
ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
ObjectCollectionProviderMorphological() - Constructor for class ObjectCollectionProviderMorphological
ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider: Base class for ObjectCollectionProvider that take a objects bean-field of same type as provided.
ObjectCollectionProviderUnary() - Constructor for class ObjectCollectionProviderUnary
ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
ObjectCollectionProviderWithFeature() - Constructor for class ObjectCollectionProviderWithFeature
ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input: Reads an ObjectCollection from the filesystem
ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties: Like an ObjectCollection but each object has associated properties.
ObjectCollectionWithProperties() - Constructor for class ObjectCollectionWithProperties
ObjectCollectionWithProperties(ObjectMask) - Constructor for class ObjectCollectionWithProperties
ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class ObjectCollectionWithProperties
ObjectCollectionWithProperties(ObjectCollection) - Constructor for class ObjectCollectionWithProperties
ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5
ObjectComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer: An object-collection to be used to compare against something
ObjectComparer() - Constructor for class ObjectComparer
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in class Base
objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter: Copies an area corresponding to an object-mask to another Voxels
ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer: A means of extracting attributes associated with a particular object (e.g.
ObjectDrawAttributes(ColorIndex) - Constructor for class ObjectDrawAttributes: Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class ObjectDrawAttributes
ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
ObjectFilter - Class in org.anchoranalysis.image.bean.object
ObjectFilter() - Constructor for class ObjectFilter
ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: A filter that combines other filters (in a list)
ObjectFilterCombine() - Constructor for class ObjectFilterCombine
ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter: Uses a predicate to make a decision whether to keep objects or not.
ObjectFilterPredicate() - Constructor for class ObjectFilterPredicate
ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter: An independent object-filter that uses a relation in its predicate.
ObjectFilterRelation() - Constructor for class ObjectFilterRelation
objectFor(T) - Method in interface AccessObjectMask: An object-mask for a given element.
ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
ObjectInputStreamDeserializer() - Constructor for class ObjectInputStreamDeserializer
ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
ObjectMask - Class in org.anchoranalysis.image.voxel.object: An object expressed in voxels, bounded within overall space.
ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates an object-mask with a corner at the origin (i.e.
ObjectMask(BoundingBox) - Constructor for class ObjectMask: Creates an object-mask to corresponding to a bounding-box with all pixels off (0)
ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask: Creates an object-mask to correspond to bounded-voxels.
ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class ObjectMask
ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class ObjectMask
ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class ObjectMask
ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge: Merges one or more ObjectMasks into a single object
ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object: A custom "stream" like class for various functional-programming operations on ObjectCollection
ObjectMaskStream(ObjectCollection) - Constructor for class ObjectMaskStream
ObjectMatcher - Class in org.anchoranalysis.image.bean.object: Matches an object with other objects.
ObjectMatcher() - Constructor for class ObjectMatcher
ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
ObjectOutputStreamGenerator() - Constructor for class ObjectOutputStreamGenerator
ObjectOutputStreamGenerator(Optional<String>) - Constructor for class ObjectOutputStreamGenerator
ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
ObjectRadiusStandardDeviation() - Constructor for class ObjectRadiusStandardDeviation
objects() - Method in class ImageInitialization
objects() - Method in class MultiInput
OBJECTS - Static variable in class OutputterDirectories: Where collections of objects are typically placed in a define-experiment output
objects(String) - Static method in class ReferenceFactory
OBJECTS_ROOT - Static variable in class HDF5PathHelper: Hardcoded string that identifies in the HDF5 file for where the object-collection is stored
OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class HDF5PathHelper: Adds seperators before and after the OBJECTS_ROOT_PATH
objectsAreAllInside(Extent) - Method in class ObjectCollection
ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Base class for generators that accept a set of objects as input.
ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class ObjectsAsGrayscaleGenerator
ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: A base class for generators that draw objects on top of a RGB-Stack.
ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class ObjectsAsRGBGenerator
ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects as a Raster with unique id values for each object.
ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class ObjectsAsUniqueValueGenerator
ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
ObjectSerializerPeriodicReporter(String) - Constructor for class ObjectSerializerPeriodicReporter
objectsForThumbnail(T) - Method in class CombineObjectsForFeatures: Selects objects from an input that will be used for thumbnail generation
objectsForThumbnail(FeatureInputSingleObject) - Method in class EachObjectIndependently
objectsForThumbnail(FeatureInputPairObjects) - Method in class PairNeighbors
ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected: Creates a ObjectCollection from the connected-components of a mask or binary-voxels.
ObjectsFromConnectedComponentsFactory() - Constructor for class ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(int) - Constructor for class ObjectsFromConnectedComponentsFactory
ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class ObjectsFromConnectedComponentsFactory
objectsFromOverlays(OverlayCollection) - Static method in class OverlayCollectionObjectFactory: Creates objects from whatever Overlays are found in the collection *
ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects merged together as a mask.
ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class ObjectsMergedAsMaskGenerator
ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class ObjectsToCompare
objectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator: The objects to draw (without any colors) on the background
objectsToDraw(Dimensions) - Method in class ColoredObjects
objectsToDraw(Dimensions) - Method in class ColoredMarks
ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge: A vertex in a merge graph representing an object (and and an associated payload)
ObjectVertex(ObjectMask, double) - Constructor for class ObjectVertex
ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Like ObjectAsMaskGenerator but additionally outputs a serialized bounding box.
ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class ObjectWithBoundingBoxGenerator
ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class ObjectWithEllipse
ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature-value from a collection.
ObjectWithMaximumFeature() - Constructor for class ObjectWithMaximumFeature
ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature: Finds the object with the maximum feature among a group of matches for each object.
ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class ObjectWithMaximumFeatureFromEachMatchedCollection
ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties: An ObjectMask with associated key-value properties.
ObjectWithProperties(BoundingBox) - Constructor for class ObjectWithProperties
ObjectWithProperties(ObjectMask) - Constructor for class ObjectWithProperties
ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class ObjectWithProperties
obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class AggregateTriggerBank
obtain(int, PeriodReceiver<S>) - Method in class PeriodTriggerBank
of(Stream<T>) - Static method in class FunctionalList: Creates a list from a stream.
of(boolean, boolean) - Static method in enum OutsideKernelPolicy: Multiplexes between all three possible enums.
of(boolean) - Static method in class NeighborhoodFactory: Gets an appropriate neighborhood
of(ObjectMask...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements from the parameter-list
of(ObjectCollection...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections
of(Optional<ObjectCollection>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections (if they exist)
of(Collection<ObjectMask>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements copied from existing collections
of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class ObjectCollectionFactory: Creates a new collection with elements from the parameter-list of BinaryVoxels converting the voxels in their entireity to an object-mask at the origin.
of(CalculationResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class CalculateShellObjectMask
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateDilation
of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
of(SessionInput<FeatureInputSingleObject>, boolean) - Static method in class CalculateEllipsoidLeastSquares
offset(int, int) - Method in class Dimensions
offset(Point3i) - Method in class Dimensions
offset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
offset(int, int) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offset(int, int, int) - Method in class Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offset(ReadableTuple3i) - Method in class Extent: Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
offset(Point2i) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
offsetGlobal(int, int) - Method in class ObjectMask
offsetRelative(int, int) - Method in class ObjectMask
offsetSlice(Point3i) - Method in class Dimensions
offsetSlice(ReadableTuple3i) - Method in class Extent: Calculates a XY-offset of a point in a buffer whose dimensions are this extent
OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer: Like a PointTwoDimensionalConsumer but also has a buffer offset.
OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer: Like a ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset value.
ofResolved(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-TIFF using the Bioformats library.
OMETiff() - Constructor for class OMETiff: Default constructor.
OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer: Writes a stack to the filesystem as an OME-XML using the Bioformats library.
OMEXML() - Constructor for class OMEXML: Default constructor.
One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects one specific channel from a set of stacks
One() - Constructor for class One
oneOnly(String, String, boolean, boolean) - Static method in class CheckMisconfigured: Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: A base-class for a raster-writer that writes only one or three channeled images, and a flexible extension.
OneOrThreeChannelsWriter() - Constructor for class OneOrThreeChannelsWriter
OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
OneStageGenerator() - Constructor for class OneStageGenerator
ongoingTasksLessThan(int) - Method in class ConcurrentJobMonitor
onInit(P) - Method in class InitializableBean: Called after initialization.
onInit(NullInitialization) - Method in class NullParamsBean
onInit() - Method in class NullParamsBean: As there's no parameters we expose a different method
onInit(DictionaryInitialization) - Method in class DictionaryProviderReference
onInit(FeatureInitialization) - Method in class Feature: Called after initialization.
onInit(FeaturesInitialization) - Method in class ReferencedFeatures
onInit(ImageInitialization) - Method in class BinarySegmentationReference
onInit() - Method in class MarkWithIdentifierFactory
onInit(ImageInitialization) - Method in class FromInput
onInit(ImageInitialization) - Method in class FromChannel
onInit(ImageInitialization) - Method in class Reference
onInit(ImageInitialization) - Method in class FromStackChannel
onInit(ImageInitialization) - Method in class ReferenceOrElse
onInit(ImageInitialization) - Method in class FromInput
onInit(FeaturesInitialization) - Method in class PermuteFeature
onInit(MarksInitialization) - Method in class FeatureValueCheckMark
onInit(MarksInitialization) - Method in class MarkProposerReference
onInit(MarksInitialization) - Method in class MarkMergeProposerReference
onInit(MarksInitialization) - Method in class MarkSplitProposerReference
onInit(MarksInitialization) - Method in class KernelMerge
onInit(PointsInitialization) - Method in class Reference
OnlyIf - Class in org.anchoranalysis.experiment.bean.log: Logs messages to a particular location ONLY if certain conditions are fulfilled.
OnlyIf() - Constructor for class OnlyIf
open() - Method in interface Progress
open() - Method in class ProgressConsole
open() - Method in class ProgressIgnore
open() - Method in class ProgressIncrement
open() - Method in class ProgressOneOfMany
open(int, Progress) - Method in interface OpenedImageFile: Open when we don't have a specific-type
open(int, Progress) - Method in class BioformatsOpenedRaster
open(Path) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(Path, String, boolean) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(Path, String, boolean, boolean) - Static method in class CSVReaderByLine: Default reader, using comma and first-line headers
open(int, Progress) - Method in class MultiFileReaderOpenedRaster
openCheckType(int, Progress, VoxelDataType) - Method in interface OpenedImageFile
OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack: Reads a stack from the file-system using OpenCV.
OpenCVReader() - Constructor for class OpenCVReader
OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack: Writes a stack to the file-system using OpenCV and a specified extension.
OpenCVWriter() - Constructor for class OpenCVWriter
OpenedCSVFile() - Constructor for class CSVReader.OpenedCSVFile
OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input: An image file that has been opened for reading containing one or more series of image-Stacks.
openFile(Path) - Method in class StackReader: Opens a file containing one or more images but does not read an image.
openFile(Path) - Method in class BioformatsReader
openFile(Path) - Method in class BranchExtension
openFile(Path) - Method in class FlattenAsChannel
openFile(Path) - Method in class ImposeResolution
openFile(Path) - Method in class MultiFileReader
openFile(Path) - Method in class ReadVoxelExtentXml
openFile(Path) - Method in class RejectIfConditionXYResolution
openFile(Path) - Method in class OpenCVReader
openMarksFromFilePath(Path) - Static method in class TestLoaderMarks
openMarksFromTestPath(String) - Method in class TestLoaderMarks
openMask(StackReader, Path, BinaryValues) - Static method in class MaskReader: Utility functions for opening a single-channeled stack as a Mask.
openXmlAbsoluteFilePath(String) - Static method in class TestLoader: Opens a XML document - with an absolute path on the filesystem
openXmlAbsoluteFilePath(Path) - Static method in class TestLoader: Opens a XML document - with an absolute path on the filesystem
openXmlFromTestPath(String) - Method in class TestLoader: Opens a XML document - with a path relative to the test root
OperationFailedException - Exception in org.anchoranalysis.core.exception
OperationFailedException(String) - Constructor for exception OperationFailedException
OperationFailedException(Throwable) - Constructor for exception OperationFailedException
OperationFailedException(String, Throwable) - Constructor for exception OperationFailedException
OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
OperationFailedRuntimeException(String) - Constructor for exception OperationFailedRuntimeException
OperationFailedRuntimeException(Exception) - Constructor for exception OperationFailedRuntimeException
OperationMap<T> - Class in org.anchoranalysis.mpp.io.input: Stores objects as operations
OperationMap() - Constructor for class OperationMap
OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class OptimizationContext
OptimizationScheme<S,U,V> - Class in org.anchoranalysis.mpp.segment.bean.optimization: An optimization-scheme that uses kernels to make changes to state.
OptimizationScheme() - Constructor for class OptimizationScheme
OptimizationStep<S,T,V> - Class in org.anchoranalysis.mpp.segment.optimization.step
OptimizationStep() - Constructor for class OptimizationStep
OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
OptimizationStepLogReporter() - Constructor for class OptimizationStepLogReporter
OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception OptimizationTerminatedEarlyException
OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation: Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
OptionalFactory - Class in org.anchoranalysis.bean: Utility functions to create Optional from nullable providers or boolean flags.
OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined: A simple container expressing a value and an associationed optional name.
OptionalNameValue(Optional<String>, V) - Constructor for class OptionalNameValue
OptionalOperationUnsupportedException - Exception in org.anchoranalysis.core.exception
OptionalOperationUnsupportedException() - Constructor for exception OptionalOperationUnsupportedException
OptionalOperationUnsupportedException(String) - Constructor for exception OptionalOperationUnsupportedException
OptionalOperationUnsupportedException(Exception) - Constructor for exception OptionalOperationUnsupportedException
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
OptionalUtilities - Class in org.anchoranalysis.core.functional: Additional utility functions for Optional and exceptions.
or(StackWriteAttributes) - Method in class StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical or on each field.
Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
Or() - Constructor for class Or
Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine: Applies multiples filter with logical OR i.e.
Or() - Constructor for class Or
order(String) - Method in interface OrderProvider
OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
OrderedList() - Constructor for class OrderedList
orderedListOfFeatures() - Method in class AddCriteriaEnergyPair
orderedListOfFeatures() - Method in class AddCriteriaNever
orderedListOfFeatures() - Method in class AddCriteriaOr
orderedListOfFeatures() - Method in class ArbitraryPointCommon
orderedListOfFeatures() - Method in class BoundingBoxIntersection
orderedListOfFeatures() - Method in interface OrderedFeatureList: A list of features used to determine the add-criteria, or null if irrelevant.
orderedListOfFeatures() - Method in class AddCriteriaFeatureRelationThreshold
OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
OrderedRadius() - Constructor for class OrderedRadius
OrderProvider - Interface in org.anchoranalysis.core.index.bounded
orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class OptionalUtilities: Like Optional.orElseGet(java.util.function.Supplier<? extends T>) but tolerates an exception in the supplier function, which is immediately thrown.
orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities: Like OptionalUtilities.orElseGet(java.util.Optional<T>, org.anchoranalysis.core.functional.checked.CheckedSupplier<T, E>) but returns a Optional and can chain many alternatives.
orFlat(CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities: The first optional if it's present, or the second, or the third etc.
org.anchoranalysis.annotation - package org.anchoranalysis.annotation: Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image: Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io: Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment: A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator: Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean: Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer: What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image: Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable: The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark: Reading and writing Mark-related annotations from/to the file-system.
org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark: Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean - package org.anchoranalysis.bean: Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation: Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define: Define and related-classes.
org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder: DefineAdder and related-classes.
org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception: Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable: Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.params - package org.anchoranalysis.bean.initializable.params: Some kinds of parameters used when initializing beans.
org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property: Performing initializion on particular properties in a bean.
org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute: Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property: Applying permutations to the properties of a bean.
org.anchoranalysis.bean.permute.setter - package org.anchoranalysis.bean.permute.setter: Setter used to impose a permutation on bean properties.
org.anchoranalysis.bean.provider - package org.anchoranalysis.bean.provider: A means of creating / loading / referencing a bean from another bean or class.
org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared: Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color: Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme: Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary: Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path: Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random: Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex: Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation: Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold: Specifies a unary relation to a *threshold* value.
org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml: Reading Beans from XML files.
org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception: Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory: Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher: Launching the anchor GUI interactive application from command-line.
org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache: Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.color - package org.anchoranalysis.core.color: Specifying particular colors and groups of colors.
org.anchoranalysis.core.concurrency - package org.anchoranalysis.core.concurrency: Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception: Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable: Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly: Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.format - package org.anchoranalysis.core.format: File formats and associated extensions.
org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional: Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked: Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph: Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter: Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name: Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider: A collection of named-elements, a NamedProvider, and related operations.
org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store: Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index - package org.anchoranalysis.core.index: Classes to support getting/setting/specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.bounded - package org.anchoranalysis.core.index.bounded: A range of elements with indiced, bounded to lie between particular a minimum and maximum.
org.anchoranalysis.core.index.bounded.bridge - package org.anchoranalysis.core.index.bounded.bridge: Exposes one type as a BoundedIndexContainer of another type.
org.anchoranalysis.core.log - package org.anchoranalysis.core.log: Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error: Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress: Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
org.anchoranalysis.core.random - package org.anchoranalysis.core.random: Generating random numbers.
org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize: Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system - package org.anchoranalysis.core.system: Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path: Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.value - package org.anchoranalysis.core.value: Encapsulating values or sets of named-values.
org.anchoranalysis.experiment - package org.anchoranalysis.experiment: Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean: Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier: Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io: Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log: Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor: How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require: A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task: Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io: Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log: Helpful classes for logging.
org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task: Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor: Non-bean classes related to JobProcessor.
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean: Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list: A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator: Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider: Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results: Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate: Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache: Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy: A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input: Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv: Writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name: Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results: Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group: Various different outputs that can be written for the a grouped version of the results in ResultsWriter.
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name: Data objects for the names of features.
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results: Results from one or more feature calculations.
org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session: A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache: Creates a FeatureSessionCache to use during feature-calculations.
org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder: Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.calculator.multi - package org.anchoranalysis.feature.session.calculator.multi: Calculates results for one or more features for a given input.
org.anchoranalysis.feature.session.calculator.single - package org.anchoranalysis.feature.session.calculator.single: Calculates results for a single feature for a given input.
org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace: Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared: Features shared for referencing among calculations.
org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store: A collection of named-Features.
org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean: Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter: Base classes for comparing a channel to another type.
org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator: Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error: Specific exception types that can be thrown in this module.
org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init: Initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment: Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange: Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object: Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider: Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack: A provider of Stacks.
org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment: Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary: Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object: Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial: Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange: Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction: Beans to specify a direction.
org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold: Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation: Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance: Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent: Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area: Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume: Converting quantities of volume between units.
org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage: Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel: The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert: Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached: Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel: Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram: Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory: Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions: Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.dimensions.size - package org.anchoranalysis.image.core.dimensions.size: Determining or changing the size of an image.
org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion: Suggestions on a size for an image.
org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask: An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine: Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge: Merges two or more entities.
org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object: The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.factory - package org.anchoranalysis.image.core.object.factory: Utilities to create ObjectMask and ObjectCollection.
org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label: Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties: An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale: Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.seed - package org.anchoranalysis.image.core.object.seed: Starting points for segmentation that are guaranteed to lie on one distinct object.
org.anchoranalysis.image.core.orientation - package org.anchoranalysis.image.core.orientation: Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.image.core.outline - package org.anchoranalysis.image.core.outline: Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.outline.traverser - package org.anchoranalysis.image.core.outline.traverser: Performs a walk on every voxel on the outline of an object-mask.
org.anchoranalysis.image.core.outline.traverser.distance - package org.anchoranalysis.image.core.outline.traverser.distance: A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
org.anchoranalysis.image.core.outline.traverser.path - package org.anchoranalysis.image.core.outline.traverser.path: A set of contiguously neighboring points along the outline of an object.
org.anchoranalysis.image.core.outline.traverser.path.merge - package org.anchoranalysis.image.core.outline.traverser.path.merge: Merging multiple ContiguousVoxelPath together.
org.anchoranalysis.image.core.outline.traverser.path.merge.strategy - package org.anchoranalysis.image.core.outline.traverser.path.merge.strategy: Strategies on which ContiguousVoxelPath should be prioritized for merging.
org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points: Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack: Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named: A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.core.stack.time - package org.anchoranalysis.image.core.stack.time: Wrapping a Stack as a TimeSequence and vice versa.
org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean: Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator: Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram: Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection: Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair: Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single: Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical: Features that convert to/from physical spatial units (e.g.
org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation: Reusable implementations of FeatureCalculation related to images.
org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator: Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged: A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input: Image-related implementations of FeatureInput.
org.anchoranalysis.image.io - package org.anchoranalysis.image.io: Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel: Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw: How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature: Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine: Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader: Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer: Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input: Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.input.series - package org.anchoranalysis.image.io.channel.input.series: Non-bean classes for reading a series of Channels from the filesystem.
org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output: Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input: Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output: Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object: Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input: Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale: Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5: Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask: Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb: Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack: Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input: Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output: Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box: Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator: Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel: Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic: Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner: Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary: The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected: Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values: Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer: A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max: Buffer for performing a Maximum Intensity Projection.
org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean: Buffer for performing a mean intensity projection.
org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive: Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice: A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert: Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2: Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype: The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter: Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate: Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory: Creates new instances of Voxels and VoxelsWrapper with specific data-types.
org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator: Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator: Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting: Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor: Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel: Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate: Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process: Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer: Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer: Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel: Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count: Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological: Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline: Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood: A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object: The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological: Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate: Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics: Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder: Thresholding operations on voxels.
org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats: Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean: Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options: User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer: Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert: Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte: Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat: Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint: Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort: Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator: Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection: Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined: Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence: Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized: Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular: Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text: Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml: Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer: Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert: Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.input - package org.anchoranalysis.io.input: Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean: Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary: Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files: Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer: Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path: Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher: Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider: Methods to provide a single file-path.
org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv: Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file: Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path: Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher: Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest: A manifest that records what outputs occur and where they occur.
org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer: Classes to read manifests from the file-system.
org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory: Entities to indicate a directory in the manifest.
org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced: Classes related to a directory that has a particular sequence of outputted filenames.
org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file: Entities to indicate a file and its role in the manifest.
org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder: Methods to search through a manifest-file to find outputs matching certain conditions.
org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match: Predicates that are useful for matching against particular type of objects in finders.
org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder: Makes a record of each file/subdirectory written as output.
org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype: Predictable patterns of indexes as used in sets of outputted files.
org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean: Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled: Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer: Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules: Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled: Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi: Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single: Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error: Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle: Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter: Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory: BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer: Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded: Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer: Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml: Outputting XML to the file-system.
org.anchoranalysis.launcher - package org.anchoranalysis.launcher: Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path: SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert: Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options: A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process: Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources: Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks: Loading and displaying pre-defined tasks.
org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic: Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation: Solving or manipulating equations.
org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram: The Histogram data class and related operations.
org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization: Mathemathical optimization algorithms.
org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation: Different kinds of binary-relations.
org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics: Data structures and algorithms to calculate statistics.
org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment: Calculates first and second image moments from a covariance matrix of points.
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean: Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound: Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation: Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark: Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory: Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points: Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter: Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer: Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider: Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap: Voxel subregions of Marks.
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
org.anchoranalysis.mpp.feature.input.memo - package org.anchoranalysis.mpp.feature.input.memo
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index: Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory: Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init: Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark: Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic: Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points: Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized: A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap: Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay: Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair: Pairs of Marks.
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer: Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error: Recording errors related to proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean: Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define: DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.kernel - package org.anchoranalysis.mpp.segment.bean.kernel: Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.mpp.segment.bean.kernel.proposer
org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
org.anchoranalysis.mpp.segment.kernel - package org.anchoranalysis.mpp.segment.kernel
org.anchoranalysis.mpp.segment.kernel.proposer - package org.anchoranalysis.mpp.segment.kernel.proposer
org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
org.anchoranalysis.overlay - package org.anchoranalysis.overlay: Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean: Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection: Collections of Overlays.
org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier: Uniquely identifying an Overlay.
org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object: An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled: Creates a scaled version of ObjectMask to use as an overlay.
org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer: Drawing an overlay on an image.
org.anchoranalysis.plot - package org.anchoranalysis.plot: Plotting data on charts.
org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean: Beans for plotting.
org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme: Color schemes associated with plots.
org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index: Non-bean plot definitions.
org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate: Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer: Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison: Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner: Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file: FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label: A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy: Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison: Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction: Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider: Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance: Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define: Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider: Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold: Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur: Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
org.anchoranalysis.plugin.image.bean.channel.convert.histogram - package org.anchoranalysis.plugin.image.bean.channel.convert.histogram
org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
org.anchoranalysis.plugin.image.bean.mask.provider.dimensions - package org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
org.anchoranalysis.plugin.image.bean.mask.provider.resize - package org.anchoranalysis.plugin.image.bean.mask.provider.resize
org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
org.anchoranalysis.plugin.image.bean.object.filter.dependent - package org.anchoranalysis.plugin.image.bean.object.filter.dependent
org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce: Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.object.segment.stack - package org.anchoranalysis.plugin.image.bean.object.segment.stack: Instance-segmentation of a Stack.
org.anchoranalysis.plugin.image.bean.params - package org.anchoranalysis.plugin.image.bean.params
org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale: Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
org.anchoranalysis.plugin.image.box - package org.anchoranalysis.plugin.image.box: Non-beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
org.anchoranalysis.plugin.image.segment - package org.anchoranalysis.plugin.image.segment
org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean: A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature: Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source: Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format: Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped: Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster: Task(s) to calculate the mean of channels grouped together.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller: Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale: Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment: Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice: Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature: Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator: Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped: Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller: Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment: Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack: Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail: Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
org.anchoranalysis.plugin.imagej.bean.interpolator - package org.anchoranalysis.plugin.imagej.bean.interpolator
org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method
org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming
org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check
org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser
org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer
org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan
org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path
org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer
org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared: Objects used in shared-state in tasks.
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml: Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier: Beans that perform classification in some way.
org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster: Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
org.anchoranalysis.plugin.mpp.bean.outline - package org.anchoranalysis.plugin.mpp.bean.outline
org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline - package org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
org.anchoranalysis.plugin.mpp.experiment - package org.anchoranalysis.plugin.mpp.experiment
org.anchoranalysis.plugin.mpp.experiment.bean - package org.anchoranalysis.plugin.mpp.experiment.bean
org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
org.anchoranalysis.plugin.mpp.experiment.bean.feature - package org.anchoranalysis.plugin.mpp.experiment.bean.feature
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
org.anchoranalysis.plugin.mpp.segment - package org.anchoranalysis.plugin.mpp.segment
org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color: Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature: Extracting features using OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.decode.instance - package org.anchoranalysis.plugin.opencv.bean.object.segment.decode.instance: Decoding the tensor output from inference into an instance segmentation.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack: Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack: Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert: Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean: Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic: Arithmetic involving features.
org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional: Conditional operations involving features.
org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list: Operations that extract a single value from a list of features.
org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range: Features that compare against a range of values.
org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace: Replaces particular values if they are returned from a feature.
org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics: Converts feature values based upon a statistical measure of distribution.
org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical: Converting to/from physical units.
org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics: Non-bean statistical operations.
org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean: Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull: Convex hull operations.
org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature: Features related to points and fitting points to conics.
org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter: Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse: FeatureCalculation related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid: FeatureCalculation related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull: Non-bean convex hull operations.
org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment: Quickly defining experiments via several assumptions, including particular file-paths.
org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive: Deriving paths from existing paths as helpful to quickly defined experiments.
org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input: Specifying inputs when quickly defining an experiment.
org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend: Appending other entities to inputs when quickly defining experiments.
org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure: Specifying a structure of subdirectories and filenames when quickly defining an experiment.
org.anchoranalysis.spatial - package org.anchoranalysis.spatial: Classes for geometry or other mathematical operations in Euclidian space.
org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis: Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box: Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point: A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer: Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rotation - package org.anchoranalysis.spatial.rotation: A matrix to apply a rotation to a point.
org.anchoranalysis.spatial.rotation.factory - package org.anchoranalysis.spatial.rotation.factory: Creates RotationMatrix in varying ways.
org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree: R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale: How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test - package org.anchoranalysis.test: Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment: Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher: Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature: Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins: Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature: A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects: Fixtures for creating object-masks and related feature-inputs.
Orientation - Class in org.anchoranalysis.image.core.orientation
Orientation() - Constructor for class Orientation
Orientation - Class in org.anchoranalysis.image.io.bean.object.draw: Writes a line through the midpoint illustrating the orientation of the object
Orientation() - Constructor for class Orientation
Orientation2D - Class in org.anchoranalysis.image.core.orientation
Orientation2D(double) - Constructor for class Orientation2D
Orientation2D() - Constructor for class Orientation2D
Orientation3DEulerAngles - Class in org.anchoranalysis.image.core.orientation
Orientation3DEulerAngles() - Constructor for class Orientation3DEulerAngles
Orientation3DEulerAngles(double, double, double) - Constructor for class Orientation3DEulerAngles
OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single: Proposes both an orientation and radii for a ConicBase
OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class OrientationAndRadiiProposer
OrientationAxisAngle - Class in org.anchoranalysis.image.core.orientation: An orientation in axis-angle representation.
OrientationAxisAngle(Vector3d, double) - Constructor for class OrientationAxisAngle
OrientationIdentity - Class in org.anchoranalysis.image.core.orientation
OrientationIdentity(int) - Constructor for class OrientationIdentity
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
OrientationProposer() - Constructor for class OrientationProposer
OrientationRotationMatrix - Class in org.anchoranalysis.image.core.orientation
OrientationRotationMatrix() - Constructor for class OrientationRotationMatrix
OrientationRotationMatrix(RotationMatrix) - Constructor for class OrientationRotationMatrix
otherVertex(V) - Method in class TypedEdge: The other vertex on the edge
Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Performs auto-thresholding using Otsu's method.
Otsu() - Constructor for class Otsu
OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold: Similar to Otsu, but weighs the variances differently of background and foreground
OtsuWeighted() - Constructor for class OtsuWeighted
OtsuWeighted(double, double) - Constructor for class OtsuWeighted
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixer: Provides a prefix which can be prepended to all output files.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class Rooted
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve: Provides a prefix which can be prepended to all output files.
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IncrementingNumber
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve: Determines the out-file prefix from a path
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class DirectoryStructure
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class FromDescriptiveName
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IfIncrementingNumberRequested
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class LastDirectoryAsPrefix
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathRegEx
outgoingEdgesFor(V) - Method in class GraphWithPayload: All outgoing edges for a given vertex.
outline(Mask, int, boolean, boolean) - Static method in class FindOutline: Creates an outline of depth 1 from a mask
outline(ObjectMask, int, boolean, boolean) - Static method in class FindOutline: Creates outline from an object
Outline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of each object-mask.
Outline() - Constructor for class Outline
Outline(int) - Constructor for class Outline
Outline(int, boolean) - Constructor for class Outline
Outline - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological: Always creates a new mask for the result (no need to duplicate input)
Outline() - Constructor for class Outline
outlineGuess3D(Mask, int, boolean, boolean) - Static method in class FindOutline: Finds the outline of a mask, guessing whether to do this in 2D or 3D depending on if the mask has 3-dimensions
OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline
OutlineKernel() - Constructor for class OutlineKernel
OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline: A base class for kernels that find the outline of an ObjectMask.
OutlineKernelBase() - Constructor for class OutlineKernelBase
OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
OutlineKernelBase() - Constructor for class OutlineKernelBase
OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline: Outputs the outline of an object-mask, but only for voxels on the exterior which neighbour a binary-mask.
OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class OutlineKernelNeighborMatchValue: Creates for an object.
OutlinePixelsRetriever - Class in org.anchoranalysis.plugin.mpp.bean.outline
OutlinePixelsRetriever() - Constructor for class OutlinePixelsRetriever
OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object: Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
OutlinePreserveRelativeSize() - Constructor for class OutlinePreserveRelativeSize
outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using a single color for all objects
OutlineTraverser - Class in org.anchoranalysis.image.core.outline.traverser
OutlineTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class OutlineTraverser
outlineVariedColors(int, int, DisplayStack) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using varied colors for the objects.
outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects on a background using varied colors for the objects.
outlineWithColorIndex(int, ColorIndex) - Static method in class DrawObjectsGenerator: A generator that draws an outline around objects using a particular color-index.
output() - Method in class ExecutionArguments: Arguments to help specify the outputs from the experiment.
output(InputOutputContext) - Method in class OutputFeatureTable: Outputs the feature-table.
output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class NamedStacksOutputter: Writes all or a subset from a set of named-stacks to a directory as a raster.
output(String, boolean) - Method in class NamedProviderOutputter: Outputs the entities using a particular output-name.
OUTPUT_BY_GROUP - Static variable in class CompareAnnotations
OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class ResultsWriterOutputNames: If not otherwise specified, the output name for a non-aggregated CSV of the results.
OUTPUT_FEATURE_TABLE - Static variable in class OutputFeatureTable
OUTPUT_MANIFEST - Static variable in class OutputExperiment
OUTPUT_MANIFEST - Static variable in class Task
OUTPUT_RESULTS - Static variable in class ExportFeatures
OUTPUT_SUMMARY_CSV - Static variable in class SharedStateSegmentInstance
OUTPUT_THUMBNAILS - Static variable in class SharedStateExportFeatures
outputAfterAllTasksAreExecuted(Outputter) - Method in interface ExperimentState
outputAfterAllTasksAreExecuted(Outputter) - Method in class SegmentMarksState
OutputArguments - Class in org.anchoranalysis.experiment.arguments: Arguments that can further specify an experiment's output in addition to its bean specification.
OutputArguments() - Constructor for class OutputArguments
outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface ExperimentState
outputBeforeAnyTasksAreExecuted(Outputter) - Method in class SegmentMarksState
OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error: When an output-directory already exists.
OutputDirectoryAlreadyExistsException(String) - Constructor for exception OutputDirectoryAlreadyExistsException
OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled: Whether a particular output, identified by a textual name, is enabled or not.
OutputEnabled() - Constructor for class OutputEnabled
OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded: Additional output-names to enable or disable from an existing set of output-enabled rules.
OutputEnabledDelta() - Constructor for class OutputEnabledDelta
OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled: A specific set of first-level outputs are enabled, to which more can be added.
OutputEnabledMutable(String...) - Constructor for class OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class OutputEnabledMutable: Creates with one or more enabled outputs.
OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules: Bean that specifies an implementation of MultiLevelOutputEnabled.
OutputEnabledRules() - Constructor for class OutputEnabledRules
OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules: Base class for an OutputEnabledRules that specifies particular output-names for first and second levels.
OutputEnableRulesSpecify(StringSet) - Constructor for class OutputEnableRulesSpecify: Create with a specific set of first-level output names.
OutputEnableRulesSpecify() - Constructor for class OutputEnableRulesSpecify
OutputExperiment - Class in org.anchoranalysis.experiment.bean.io: An experiment that uses a OutputManager to specify the outputting of results.
OutputExperiment() - Constructor for class OutputExperiment
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for outputs.
OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature: Specifies a table of feature-calculations on objects.
OutputFeatureTable() - Constructor for class OutputFeatureTable
outputFormatString() - Method in class IndexableOutputNameStyle
outputFormatString() - Method in class IntegerSuffixOutputNameStyle
outputFormatString() - Method in class StringSuffixOutputNameStyle
outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class GroupMapByName: Outputs the "grouped" data to the filesystem
outputHeaderToWriter(PrintWriter, String) - Method in class AggIDCounter
outputHeaderToWriter(PrintWriter) - Method in class Aggregator
OutputManager - Class in org.anchoranalysis.io.output.bean: Responsible for making decisions on where output goes and what form it takes.
OutputManager() - Constructor for class OutputManager
outputName(String) - Static method in class FileMatch: Match a file whose output-name matches a specific value.
outputNameForGroups() - Method in class GroupedStackBase: The first-level output-name used for determining if groups are written.
outputNameForGroups() - Method in class ExportImageHistograms
outputNameForGroups() - Method in class GroupedMeanChannelTask
outputNames() - Method in class ResultsWriterMetadata: Names for any outputs produced by ResultsWriter.
OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
OutputNameStyle(String) - Constructor for class OutputNameStyle
OutputNameStyle() - Constructor for class OutputNameStyle
OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern: A particular naming pattern files follow when outputted.
OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class OutputPattern
OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing integer index.
OutputPatternIntegerSuffix(String, boolean) - Constructor for class OutputPatternIntegerSuffix: Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
OutputPatternIntegerSuffix(String, String) - Constructor for class OutputPatternIntegerSuffix: Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, boolean) but with additional options on the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Like OutputPatternIntegerSuffix(String, String) but with additional options about the number of digits, the manifest-folder description and whether to check outputs against rules.
OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix: Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern: A OutputPattern that outputs a file-name with a trailing string index.
OutputPatternStringSuffix(String, boolean) - Constructor for class OutputPatternStringSuffix: Creates without a prefix.
OutputPatternStringSuffix(String, boolean, String) - Constructor for class OutputPatternStringSuffix: Creates with a prefix.
OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer: Arguments influencing into which directory outputs are written, and how identifiers are expressed.
OutputPrefixerSettings() - Constructor for class OutputPrefixerSettings
OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files using whatever prefix is assigned to an input by the OutputManager as the file-name, adding the same extension as the source file.
OutputPrefixWithExtension() - Constructor for class OutputPrefixWithExtension
outputSelectParam(CommandLine) - Static method in class SelectParamFactory: Can point to either: a path ending in .xml, assumed to BeanXML for an output manager a directory, set as the outputDirectory in the input-context
outputsEnabled() - Method in class Outputter
OutputSequence - Interface in org.anchoranalysis.io.generator.sequence: A sequence of elements that are written to the same directory.
OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence: Creates and starts a OutputSequence with a particular generator and context.
OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class OutputSequenceFactory
OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class OutputSequenceIncrementing
OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence: A sequence of outputs that use the same generator with non-incrementing indexes for each output.
OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output: Creates OutputSequence of different kinds for writing stacks to a directory.
outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class DefineOutputter
OutputtedFile - Class in org.anchoranalysis.io.manifest.file: An entry in a Manifest for an outputted file from an experiment.
OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class OutputtedFile
OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class OutputtedFile
Outputter - Class in org.anchoranalysis.io.output.outputter: Like OutputterChecked but exceptions are reported in a ErrorReporter.
Outputter(OutputterChecked, ErrorReporter) - Constructor for class Outputter
OutputterChecked - Class in org.anchoranalysis.io.output.outputter: A particular directory on the filesystem in which outputting can occur.
OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define: Directories into which collections of different types of objects are written to in a define experiment
OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory: The directory and prefix an outputter writes to.
OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class OutputterTarget
outputToWriter(PrintWriter) - Method in class AggIDCounter
outputToWriter(PrintWriter) - Method in class Aggregator
OutputWriteContext - Class in org.anchoranalysis.io.output.outputter: Settings and user-arguments for writing files.
OutputWriteContext() - Constructor for class OutputWriteContext
OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>) - Constructor for class OutputWriteContext
OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
OutputWriteFailedException(String) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception OutputWriteFailedException
OutputWriteFailedException(Throwable) - Constructor for exception OutputWriteFailedException
OutputWriteSettings - Class in org.anchoranalysis.io.output.bean: Settings for how to write output, including default writers.
OutputWriteSettings() - Constructor for class OutputWriteSettings
OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel: How to handle voxels whose neighbours are outside ths scene.
OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
OutsideRange() - Constructor for class OutsideRange
overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateKernelHelper
OverlapCalculator - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce: Calculates overlap between object-masks
OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMaskBase() - Constructor for class OverlapMaskBase
OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapMIPBase() - Constructor for class OverlapMIPBase
OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumVoxels() - Constructor for class OverlapNumVoxels
OverlapNumVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapNumVoxelsMask() - Constructor for class OverlapNumVoxelsMask
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class FeaturePairMemoSingleRegion
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMIPBase
OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label: An object-mask that is founded to overlap with another during labelling.
OverlappingObject(T, ObjectMask) - Constructor for class OverlappingObject
OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatio() - Constructor for class OverlapRatio
OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
OverlapRatioMask() - Constructor for class OverlapRatioMask
OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Expresses the number of intersecting pixels between two objects as a ratio to something else (denominator)
OverlapRelative() - Constructor for class OverlapRelative
OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToFirst() - Constructor for class OverlapRelativeToFirst
OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap: Overlap ratio to the maximum number of pixels
OverlapRelativeToMaxVolume() - Constructor for class OverlapRelativeToMaxVolume
OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToMerged() - Constructor for class OverlapRelativeToMerged
OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
OverlapRelativeToSecond() - Constructor for class OverlapRelativeToSecond
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class OverlapUtilities
overlapWithGlobalMask(SessionInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class OverlapUtilities: Counts the number of overlapping voxels between two VoxelizedMarkMemo
Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange: Overlays one image on the other.
Overlay() - Constructor for class Overlay
Overlay(String, String, String) - Constructor for class Overlay
Overlay - Class in org.anchoranalysis.overlay: An entity that will eventually be drawn on top of an image.
Overlay() - Constructor for class Overlay
overlayBufferedImage(BufferedImage, BufferedImage, int, int) - Static method in class BufferedImageOverlay
OverlayCollection - Class in org.anchoranalysis.overlay.collection
OverlayCollection() - Constructor for class OverlayCollection
OverlayCollection(Stream<Overlay>) - Constructor for class OverlayCollection
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay: Two-way factory.
OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection: Two-way factory.
OverlayMark - Class in org.anchoranalysis.mpp.overlay
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class OverlayMark
OverlayObjectMask - Class in org.anchoranalysis.overlay.object
OverlayObjectMask(ObjectMask, int) - Constructor for class OverlayObjectMask
OverlayProperties - Class in org.anchoranalysis.overlay
OverlayProperties() - Constructor for class OverlayProperties

P

Q

R

S

T

U

V

W

X

x() - Method in class Dimensions
x() - Method in class Resolution
x() - Method in class DirectionVector
x(int) - Method in class BoundingBoxContains: Is this value in the x-dimension within the bounding box range?
x() - Method in class Extent
x() - Method in class Point2d
x() - Method in class Point2f
x() - Method in class Point2i
x() - Method in interface ReadableTuple3i
x - Variable in class Tuple3d
x() - Method in class Tuple3d
x - Variable in class Tuple3f
x() - Method in class Tuple3f
x(float) - Method in class Tuple3f
x - Variable in class Tuple3i
x() - Method in class Tuple3i
x() - Method in class ScaleFactor: How much to multiply the existing x-dimension by to create a scaled x-dimension.
xFromChainCode(int) - Static method in class ChainCodesDirection
XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml
XMLGenerator() - Constructor for class XMLGenerator
XMLUtilities - Class in org.anchoranalysis.core.serialize
XMLWriter - Class in org.anchoranalysis.io.output.xml
Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine: Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
Xor() - Constructor for class Xor
XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize: Deserializes an object using the XStream library.
XStreamDeserializer() - Constructor for class XStreamDeserializer
XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
XStreamGenerator() - Constructor for class XStreamGenerator
XStreamGenerator(Optional<String>) - Constructor for class XStreamGenerator
XStreamSerializer - Class in org.anchoranalysis.core.serialize: Serializes an object using the XStream library.
XYOrientationExtendToZ - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
XYOrientationExtendToZ() - Constructor for class XYOrientationExtendToZ

Y

y() - Method in class Dimensions
y() - Method in class Resolution
y() - Method in class DirectionVector
y(int) - Method in class BoundingBoxContains: Is this value in the y-dimension within the bounding box range?
y() - Method in class Extent
y() - Method in class Point2d
y() - Method in class Point2f
y() - Method in class Point2i
y() - Method in interface ReadableTuple3i
y - Variable in class Tuple3d
y() - Method in class Tuple3d
y - Variable in class Tuple3f
y() - Method in class Tuple3f
y(float) - Method in class Tuple3f
y - Variable in class Tuple3i
y() - Method in class Tuple3i
y() - Method in class ScaleFactor: How much to multiply the existing y-dimension by to create a scaled y-dimension.
yFromChainCode(int) - Static method in class ChainCodesDirection

Z

z() - Method in class Dimensions
z() - Method in class Resolution
z() - Method in class DirectionVector
z(int) - Method in class BoundingBoxContains: Is this value in the z-dimension within the bounding box range?
z() - Method in class Extent
z() - Method in interface ReadableTuple3i
z - Variable in class Tuple3d
z() - Method in class Tuple3d
z - Variable in class Tuple3f
z() - Method in class Tuple3f
z(float) - Method in class Tuple3f
z - Variable in class Tuple3i
z() - Method in class Tuple3i
zChange - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask: Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
ZeroOutsideMask() - Constructor for class ZeroOutsideMask
zeroValue(int) - Method in class Histogram
zFromChainCode(int) - Static method in class ChainCodesDirection
zIfDefined(double) - Method in class Resolution: Returns the z-resolution like Resolution.z() if the z-resolution is not NaN.
zip(Collection<S>, Collection<T>) - Static method in class FunctionalList: Create a list of pairs of elements from two separate collections.
zRelative() - Method in class Resolution: Assumes x and y has constant resolution, and gives the relative resolution of z to x or y.
zScore(double) - Method in class FirstSecondOrderStatistic
ZScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
ZScore() - Constructor for class ZScore

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